Available Modules
Modules are the building stones of all DSL2 nf-core blocks. You can find more info from nf-core website, if you would like to write your own module.
- metagenomics 91
- genomics 23
- fastq 20
- classify 20
- bam 19
- classification 19
- taxonomic profiling 18
- database 17
- alignment 11
- assembly 10
- download 10
- taxonomy 10
- taxonomic classification 10
- sort 9
- long reads 9
- fasta 8
- coverage 8
- binning 8
- kmer 8
- metagenome 8
- db 8
- contamination 7
- quality 7
- build 7
- mags 7
- completeness 7
- virus 7
- checkm 7
- mag 7
- kraken2 7
- genome 6
- contigs 6
- visualisation 6
- phage 6
- mapping 6
- markduplicates 6
- kmers 6
- vsearch 6
- index 5
- cram 5
- bacteria 5
- statistics 5
- sequences 5
- bins 5
- complexity 5
- sketch 5
- ptr 5
- isolates 5
- sourmash 5
- coptr 5
- profiling 5
- microbiome 5
- gatk4 4
- sam 4
- merge 4
- k-mer 4
- ancient DNA 4
- table 4
- aDNA 4
- archaeogenomics 4
- palaeogenomics 4
- diversity 4
- malt 4
- ganon 4
- skani 4
- redundancy 4
- umitools 4
- clustering 3
- search 3
- population genetics 3
- dedup 3
- profile 3
- report 3
- antimicrobial resistance genes 3
- distance 3
- de novo assembly 3
- merging 3
- bin 3
- abundance 3
- containment 3
- UMI 3
- amplicon sequences 3
- vrhyme 3
- kraken 3
- bracken 3
- sylph 3
- checkv 3
- vcf 2
- annotation 2
- nanopore 2
- pacbio 2
- bcftools 2
- isoseq 2
- long-read 2
- imaging 2
- depth 2
- antimicrobial resistance 2
- damage 2
- ncbi 2
- peaks 2
- plasmid 2
- deduplication 2
- prediction 2
- detection 2
- arg 2
- compare 2
- telomere 2
- deep learning 2
- deeparg 2
- host 2
- microbes 2
- krona chart 2
- dist 2
- profiles 2
- krakentools 2
- split_kmers 2
- barcode 2
- iphop 2
- krakenuniq 2
- link 2
- taxon tables 2
- otu tables 2
- standardisation 2
- standardise 2
- ome-tif 2
- MCMICRO 2
- signature 2
- FracMinHash sketch 2
- metamaps 2
- taxonomic profile 2
- metagenomic 2
- MaltExtract 2
- HOPS 2
- authentication 2
- edit distance 2
- single cells 2
- genome bins 2
- metagenomes 2
- genomad 2
- bed 1
- filter 1
- map 1
- gtf 1
- split 1
- sentieon 1
- count 1
- VCF 1
- copy number 1
- imputation 1
- rnaseq 1
- trimming 1
- reporting 1
- indexing 1
- QC 1
- metrics 1
- repeat 1
- example 1
- plot 1
- amr 1
- cluster 1
- machine learning 1
- iCLIP 1
- umi 1
- antimicrobial peptides 1
- extract 1
- duplicates 1
- visualization 1
- cat 1
- amps 1
- FASTQ 1
- fragment 1
- antibiotic resistance 1
- riboseq 1
- ccs 1
- normalization 1
- add 1
- retrotransposon 1
- hybrid capture sequencing 1
- copy number alteration calling 1
- DNA sequencing 1
- targeted sequencing 1
- bedgraph 1
- fgbio 1
- arriba 1
- spark 1
- html 1
- fusion 1
- rsem 1
- genome mining 1
- hi-c 1
- gatk4spark 1
- comparison 1
- krona 1
- atac-seq 1
- chip-seq 1
- population genomics 1
- interactive 1
- primer 1
- instrain 1
- long terminal repeat 1
- dereplicate 1
- salmon 1
- orf 1
- registration 1
- contig 1
- sequenzautils 1
- varcal 1
- scaffold 1
- trim 1
- identifier 1
- RNA-Seq 1
- UMIs 1
- dereplication 1
- microbial genomics 1
- drep 1
- md 1
- nm 1
- uq 1
- melon 1
- extractunbinned 1
- linkbins 1
- sintax 1
- vsearch/sort 1
- usearch 1
- chromap 1
- quality assurnce 1
- qa 1
- postprocessing 1
- confidence 1
- sorted 1
- taxonomic composition 1
- prepare 1
- catpack 1
- multiqc 1
- vsearch/dereplicate 1
- Staging 1
- vsearch/fastqfilter 1
- fastqfilter 1
- CRISPRi 1
- tag2tag 1
- drug categorization 1
- impute-info 1
- tags 1
- 16S 1
- standard 1
- haplotag 1
- staging 1
- post Post-processing 1
- metagenome assembler 1
- source tracking 1
- tag 1
- cell_barcodes 1
- rna velocity 1
- cobra 1
- extension 1
- duplicate removal 1
- maxbin2 1
- metagenome-assembled genomes 1
- megahit 1
- denovo 1
- debruijn 1
- vqsr 1
- variant quality score recalibration 1
- AMP 1
- peptide prediction 1
- metaphlan 1
- otu table 1
- bgc 1
- splitcram 1
- GTDB taxonomy 1
- genome taxonomy database 1
- archaea 1
- combining 1
- gc_wiggle 1
- calmd 1
- peak-caller 1
- cut&tag 1
- cut&run 1
- chromatin 1
- seacr 1
- assembly-binning 1
- applyvarcal 1
- VQSR 1
- fracminhash sketch 1
- hash sketch 1
- nucleotide composition 1
- concoct 1
- signatures 1
- duplicate marking 1
- ARGs 1
- antibiotic resistance genes 1
- pcr 1
- groupreads 1
- consensus sequence 1
- ChIP-Seq 1
- phantom peaks 1
- illumina datasets 1
- phylogenetic composition 1
- multimapper 1
- LCA 1
- Ancestor 1
- intervals coverage 1
- reference 0
- structural variants 0
- variant calling 0
- align 0
- gff 0
- variants 0
- qc 0
- quality control 0
- cnv 0
- MSA 0
- variant 0
- gfa 0
- somatic 0
- conversion 0
- convert 0
- proteomics 0
- single-cell 0
- phylogeny 0
- bedtools 0
- graph 0
- bisulfite 0
- sv 0
- gvcf 0
- variation graph 0
- methylation 0
- databases 0
- wgs 0
- bisulphite 0
- methylseq 0
- picard 0
- compression 0
- protein 0
- bqsr 0
- illumina 0
- cna 0
- consensus 0
- stats 0
- tsv 0
- serotype 0
- 5mC 0
- demultiplex 0
- openms 0
- DNA methylation 0
- base quality score recalibration 0
- protein sequence 0
- histogram 0
- searching 0
- scWGBS 0
- pairs 0
- samtools 0
- WGBS 0
- haplotype 0
- filtering 0
- structure 0
- plink 0
- pangenome graph 0
- matrix 0
- expression 0
- neural network 0
- bisulfite sequencing 0
- mappability 0
- transcriptome 0
- aligner 0
- LAST 0
- bwa 0
- plink2 0
- low-coverage 0
- transcript 0
- genotype 0
- bcf 0
- seqkit 0
- cooler 0
- phasing 0
- gzip 0
- germline 0
- annotate 0
- sequence 0
- validation 0
- gene 0
- mmseqs2 0
- biscuit 0
- decompression 0
- hmmer 0
- ucsc 0
- gff3 0
- feature 0
- spatial 0
- newick 0
- genotyping 0
- segmentation 0
- evaluation 0
- msa 0
- blast 0
- bismark 0
- mkref 0
- glimpse 0
- hmmsearch 0
- pangenome 0
- reads 0
- json 0
- demultiplexing 0
- mitochondria 0
- cnvkit 0
- snp 0
- differential 0
- multiple sequence alignment 0
- low frequency variant calling 0
- prokaryote 0
- bedGraph 0
- short-read 0
- scRNA-seq 0
- single 0
- splicing 0
- NCBI 0
- tumor-only 0
- mirna 0
- benchmark 0
- deamination 0
- mem 0
- concatenate 0
- interval 0
- single cell 0
- tabular 0
- fastx 0
- csv 0
- de novo 0
- text 0
- mutect2 0
- kallisto 0
- summary 0
- ont 0
- call 0
- MAF 0
- counts 0
- indels 0
- svtk 0
- structural 0
- wxs 0
- idXML 0
- adapters 0
- mpileup 0
- reference-free 0
- 3-letter genome 0
- clipping 0
- query 0
- gridss 0
- view 0
- family 0
- bedpe 0
- preprocessing 0
- ngscheckmate 0
- genome assembler 0
- matching 0
- fai 0
- bigwig 0
- read depth 0
- ampir 0
- fungi 0
- peak-calling 0
- CLIP 0
- dna 0
- diamond 0
- circrna 0
- rna 0
- microarray 0
- ATAC-seq 0
- microsatellite 0
- union 0
- miscoding lesions 0
- isomir 0
- compress 0
- palaeogenetics 0
- archaeogenetics 0
- bgzip 0
- interval_list 0
- hic 0
- paf 0
- cut 0
- haplotypecaller 0
- resistance 0
- pypgx 0
- HMM 0
- enrichment 0
- chromosome 0
- gsea 0
- logratio 0
- happy 0
- STR 0
- HiFi 0
- chunk 0
- biosynthetic gene cluster 0
- bcl2fastq 0
- propr 0
- hmmcopy 0
- image 0
- parsing 0
- quantification 0
- BGC 0
- public datasets 0
- clean 0
- ranking 0
- phylogenetic placement 0
- xeniumranger 0
- SV 0
- genmod 0
- transcriptomics 0
- DNA sequence 0
- mtDNA 0
- sample 0
- sequencing 0
- ancestry 0
- snps 0
- fcs-gx 0
- macrel 0
- mlst 0
- amplify 0
- fastk 0
- das tool 0
- structural_variants 0
- C to T 0
- DRAMP 0
- das_tool 0
- angsd 0
- insert 0
- fam 0
- bim 0
- SNP 0
- small indels 0
- subsample 0
- pangolin 0
- panel 0
- pan-genome 0
- pairsam 0
- duplication 0
- prokaryotes 0
- replace 0
- bacterial 0
- covid 0
- benchmarking 0
- dictionary 0
- lineage 0
- polishing 0
- indel 0
- PCA 0
- mapper 0
- fingerprint 0
- prokka 0
- regions 0
- typing 0
- RNA-seq 0
- genomes 0
- neubi 0
- entrez 0
- eukaryotes 0
- scores 0
- seqtk 0
- mcmicro 0
- aln 0
- bwameth 0
- npz 0
- windowmasker 0
- bakta 0
- nucleotide 0
- highly_multiplexed_imaging 0
- mkfastq 0
- image_analysis 0
- cellranger 0
- gene expression 0
- zip 0
- unzip 0
- uncompress 0
- untar 0
- mask 0
- RNA 0
- rna_structure 0
- proteome 0
- guide tree 0
- long_read 0
- somatic variants 0
- transposons 0
- complement 0
- roh 0
- transcripts 0
- organelle 0
- remove 0
- converter 0
- intervals 0
- genome assembly 0
- mzml 0
- chimeras 0
- PacBio 0
- comparisons 0
- combine 0
- quality trimming 0
- score 0
- adapter trimming 0
- popscle 0
- pileup 0
- genotype-based deconvoltion 0
- bamtools 0
- variant_calling 0
- hidden Markov model 0
- archiving 0
- minimap2 0
- amplicon sequencing 0
- notebook 0
- reports 0
- ataqv 0
- informative sites 0
- kinship 0
- identity 0
- relatedness 0
- repeat expansion 0
- virulence 0
- cut up 0
- survivor 0
- miRNA 0
- cool 0
- pseudoalignment 0
- dump 0
- lossless 0
- observations 0
- shapeit 0
- khmer 0
- CRISPR 0
- prefetch 0
- spaceranger 0
- wastewater 0
- wig 0
- tabix 0
- ambient RNA removal 0
- ligate 0
- cfDNA 0
- uLTRA 0
- png 0
- gstama 0
- ichorcna 0
- mash 0
- tama 0
- pigz 0
- bustools 0
- refine 0
- resolve_bioscience 0
- gene set 0
- trancriptome 0
- gene set analysis 0
- spatial_transcriptomics 0
- lofreq 0
- screen 0
- phase 0
- haplotypes 0
- reformat 0
- serogroup 0
- minhash 0
- GC content 0
- maximum likelihood 0
- megan 0
- polyA_tail 0
- hla 0
- hlala 0
- k-mer frequency 0
- hla_typing 0
- hlala_typing 0
- checksum 0
- corrupted 0
- tree 0
- nanostring 0
- mapcounter 0
- nacho 0
- haplogroups 0
- mRNA 0
- find 0
- pair 0
- trgt 0
- cgMLST 0
- regression 0
- taxids 0
- SimpleAF 0
- taxon name 0
- zlib 0
- differential expression 0
- variation 0
- vg 0
- vcflib 0
- ampgram 0
- amptransformer 0
- orthologs 0
- WGS 0
- image_processing 0
- standardization 0
- repeats 0
- svdb 0
- de novo assembler 0
- small genome 0
- interactions 0
- functional analysis 0
- join 0
- reformatting 0
- function 0
- pharokka 0
- bloom filter 0
- k-mer index 0
- COBS 0
- archive 0
- xz 0
- mudskipper 0
- long terminal retrotransposon 0
- transcriptomic 0
- kma 0
- parallelized 0
- orthology 0
- rrna 0
- genetics 0
- tnhaplotyper2 0
- rgfa 0
- small variants 0
- multiallelic 0
- nucleotides 0
- cnvnator 0
- proportionality 0
- mitochondrion 0
- leviosam2 0
- lift 0
- mirdeep2 0
- cancer genomics 0
- homoploymer 0
- ped 0
- Duplication purging 0
- purge duplications 0
- library 0
- preseq 0
- adapter 0
- import 0
- doublets 0
- variant pruning 0
- anndata 0
- bfiles 0
- subset 0
- gene labels 0
- read-group 0
- hostile 0
- duplicate 0
- decontamination 0
- GPU-accelerated 0
- graph layout 0
- human removal 0
- screening 0
- nextclade 0
- removal 0
- msisensor-pro 0
- cleaning 0
- micro-satellite-scan 0
- tumor 0
- msi 0
- instability 0
- MSI 0
- Read depth 0
- RNA sequencing 0
- soft-clipped clusters 0
- snpsift 0
- snpeff 0
- effect prediction 0
- shigella 0
- switch 0
- ancient dna 0
- Streptococcus pneumoniae 0
- transformation 0
- rename 0
- salmonella 0
- smrnaseq 0
- fusions 0
- Pharmacogenetics 0
- fixmate 0
- retrotransposons 0
- dict 0
- collate 0
- bam2fq 0
- frame-shift correction 0
- long-read sequencing 0
- scaffolding 0
- rtgtools 0
- sequence analysis 0
- junctions 0
- pharmacogenetics 0
- runs_of_homozygosity 0
- polish 0
- assembly evaluation 0
- concordance 0
- duplex 0
- deconvolution 0
- bayesian 0
- merge mate pairs 0
- reads merging 0
- short reads 0
- xenograft 0
- graft 0
- unaligned 0
- fetch 0
- realignment 0
- GEO 0
- microscopy 0
- expansionhunterdenovo 0
- repeat_expansions 0
- metadata 0
- tab 0
- microbial 0
- allele-specific 0
- emboss 0
- panelofnormals 0
- gatk 0
- joint genotyping 0
- secondary metabolites 0
- NRPS 0
- RiPP 0
- interval list 0
- evidence 0
- antibiotics 0
- antismash 0
- filtermutectcalls 0
- simulate 0
- artic 0
- aggregate 0
- demultiplexed reads 0
- concat 0
- tbi 0
- gwas 0
- CNV 0
- sra-tools 0
- settings 0
- BAM 0
- blastn 0
- version 0
- correction 0
- calling 0
- cnv calling 0
- immunoprofiling 0
- structural-variant calling 0
- cvnkit 0
- estimation 0
- vdj 0
- recombination 0
- eCLIP 0
- splice 0
- parse 0
- fasterq-dump 0
- awk 0
- intersect 0
- intersection 0
- normalize 0
- norm 0
- scatter 0
- reheader 0
- eigenstrat 0
- validate 0
- samplesheet 0
- format 0
- eido 0
- windows 0
- blastp 0
- deseq2 0
- rna-seq 0
- region 0
- heatmap 0
- sizes 0
- bases 0
- spatial_omics 0
- random forest 0
- allele 0
- gem 0
- ChIP-seq 0
- baf 0
- getfasta 0
- derived alleles 0
- sequence search 0
- tnfilter 0
- covariance model 0
- jaccard 0
- overlap 0
- array_cgh 0
- cytosure 0
- decomposeblocksub 0
- ancestral alleles 0
- gprofiler2 0
- gost 0
- genomecov 0
- closest 0
- rad 0
- bamtobed 0
- sorting 0
- structural variant 0
- bam2fastx 0
- bam2fastq 0
- immcantation 0
- airrseq 0
- vector 0
- site frequency spectrum 0
- immunoinformatics 0
- f coefficient 0
- bioawk 0
- unionBedGraphs 0
- reverse complement 0
- simulation 0
- hmmfetch 0
- decompose 0
- pca 0
- pruning 0
- subtract 0
- linkage equilibrium 0
- slopBed 0
- transmembrane 0
- genome graph 0
- chunking 0
- tnseq 0
- homozygous genotypes 0
- decoy 0
- heterozygous genotypes 0
- htseq 0
- inbreeding 0
- shiftBed 0
- multinterval 0
- sompy 0
- overlapped bed 0
- maskfasta 0
- peak picking 0
- homology 0
- co-orthology 0
- clumping fastqs 0
- deduping 0
- plastid 0
- smaller fastqs 0
- resfinder 0
- resistance genes 0
- raw 0
- mgf 0
- parquet 0
- parser 0
- dbsnp 0
- standardize 0
- quarto 0
- masking 0
- python 0
- r 0
- low-complexity 0
- coexpression 0
- correlation 0
- corpcor 0
- GFF/GTF 0
- assay 0
- trio binning 0
- tandem repeats 0
- phylogenetics 0
- minimum_evolution 0
- parallel 0
- csi 0
- Read coverage histogram 0
- biallelic 0
- sequence similarity 0
- spectral clustering 0
- agat 0
- longest 0
- comparative genomics 0
- isoform 0
- autozygosity 0
- homozygosity 0
- deep variant 0
- variancepartition 0
- mutect 0
- idx 0
- update header 0
- intron 0
- dream 0
- transform 0
- gaps 0
- introns 0
- install 0
- joint-genotyping 0
- genotypegvcf 0
- BCF 0
- short 0
- file manipulation 0
- plink2_pca 0
- propd 0
- verifybamid 0
- vcf2db 0
- gemini 0
- maf 0
- lua 0
- toml 0
- plant 0
- vcfbreakmulti 0
- uniq 0
- deduplicate 0
- SINE 0
- VCFtools 0
- network 0
- downsample bam 0
- DNA contamination estimation 0
- wget 0
- mkvdjref 0
- construct 0
- graph projection to vcf 0
- cellpose 0
- hifi 0
- Assembly 0
- subsample bam 0
- downsample 0
- unmarkduplicates 0
- bedtobigbed 0
- genepred 0
- refflat 0
- gtftogenepred 0
- ucsc/liftover 0
- mobile genetic elements 0
- genome annotation 0
- trna 0
- covariance models 0
- umicollapse 0
- snv 0
- scanner 0
- scRNA-Seq 0
- crispr 0
- antibody capture 0
- files 0
- antigen capture 0
- helitron 0
- multiomics 0
- remove samples 0
- upd 0
- uniparental 0
- disomy 0
- domains 0
- long read alignment 0
- nucleotide sequence 0
- tnscope 0
- copyratios 0
- comp 0
- denoisereadcounts 0
- readwriter 0
- dnamodelapply 0
- dnascope 0
- tblastn 0
- bedcov 0
- genome polishing 0
- groupby 0
- assembly polishing 0
- genotype dosages 0
- vcf file 0
- bgen 0
- subtyping 0
- chloroplast 0
- blat 0
- alr 0
- clr 0
- Salmonella enterica 0
- boxcox 0
- bgen file 0
- Escherichia coli 0
- createreadcountpanelofnormals 0
- workflow_mode 0
- pangenome-scale 0
- yahs 0
- all versus all 0
- mashmap 0
- wavefront 0
- whamg 0
- wham 0
- compartments 0
- copy-number 0
- copy number analysis 0
- gender determination 0
- topology 0
- copy number alterations 0
- copy number variation 0
- geo 0
- workflow 0
- mapad 0
- adna 0
- c to t 0
- cumulative coverage 0
- proteus 0
- readproteingroups 0
- calder2 0
- eigenvectors 0
- hicPCA 0
- sliding 0
- cadd 0
- snakemake 0
- distance-based 0
- long read 0
- homologs 0
- telseq 0
- admixture 0
- mzML 0
- microRNA 0
- mass_error 0
- search engine 0
- poolseq 0
- variant-calling 0
- stardist 0
- ATACseq 0
- shift 0
- ATACshift 0
- http(s) 0
- utility 0
- setgt 0
- jvarkit 0
- translate 0
- tar 0
- tarball 0
- adapterremoval 0
- HLA 0
- nanoq 0
- Read filters 0
- Read trimming 0
- Read report 0
- hhsuite 0
- ATLAS 0
- uniques 0
- Illumina 0
- functional 0
- sequencing_bias 0
- mkarv 0
- hashing-based deconvolution 0
- rank 0
- java 0
- script 0
- post mortem damage 0
- xml 0
- svg 0
- atlas 0
- targz 0
- Computational Immunology 0
- bias 0
- scanpy 0
- nuclear contamination estimate 0
- resegment 0
- morphology 0
- fix 0
- malformed 0
- partitioning 0
- chip 0
- updatedata 0
- run 0
- model 0
- AMPs 0
- allele counts 0
- antimicrobial peptide prediction 0
- plotting 0
- regtools 0
- leafcutter 0
- amp 0
- pdb 0
- recovery 0
- mgi 0
- Staphylococcus aureus 0
- affy 0
- block substitutions 0
- reference panels 0
- relabel 0
- cell segmentation 0
- Bioinformatics Tools 0
- quality_control 0
- bclconvert 0
- nucBed 0
- AT content 0
- Immune Deconvolution 0
- nucleotide content 0
- elfasta 0
- elprep 0
- doublet 0
- patterns 0
- controlstatistics 0
- emoji 0
- regex 0
- nuclear segmentation 0
- paired reads re-pairing 0
- installation 0
- doublet_detection 0
- barcodes 0
- doCounts 0
- subsetting 0
- logFC 0
- significance statistic 0
- p-value 0
- scvi 0
- solo 0
- import segmentation 0
- redundant 0
- hmmpress 0
- identity-by-descent 0
- go 0
- scimap 0
- Bayesian 0
- host removal 0
- structural-variants 0
- omics 0
- biological activity 0
- bamtools/split 0
- prior knowledge 0
- haploype 0
- mygene 0
- yaml 0
- associations 0
- impute 0
- bedgraphtobigwig 0
- bamtools/convert 0
- reference compression 0
- pile up 0
- mouse 0
- reference panel 0
- bacphlip 0
- virulent 0
- nanopore sequencing 0
- spatial_neighborhoods 0
- Indel 0
- grea 0
- seqfu 0
- multi-tool 0
- predict 0
- background_correction 0
- illumiation_correction 0
- hardy-weinberg 0
- hwe statistics 0
- hwe equilibrium 0
- reference-independent 0
- genotype likelihood 0
- collapse 0
- liftover 0
- probabilistic realignment 0
- n50 0
- case/control 0
- cell_type_identification 0
- cell_phenotyping 0
- machine_learning 0
- element 0
- trimBam 0
- bamUtil 0
- shuffleBed 0
- SNV 0
- clahe 0
- refresh 0
- association 0
- GWAS 0
- temperate 0
- read group 0
- cram-size 0
- bwamem2 0
- bwameme 0
- grabix 0
- ribosomal 0
- 10x 0
- background 0
- single-stranded 0
- regulatory network 0
- ancientDNA 0
- transcription factors 0
- paraphase 0
- selector 0
- size 0
- Pacbio 0
- quality check 0
- realign 0
- circular 0
- phylogenies 0
- hmmscan 0
- spot 0
- orthogroup 0
- authentict 0
- sage 0
- mass spectrometry 0
- featuretable 0
- extraction 0
- guidetree 0
- AC/NS/AF 0
- functional enrichment 0
- autofluorescence 0
- translation 0
- paired reads merging 0
- overlap-based merging 0
- check 0
- lifestyle 0
- hamming-distance 0
- hashing-based deconvoltion 0
- gnu 0
- coreutils 0
- generic 0
- transposable element 0
- retrieval 0
- cycif 0
- vcflib/vcffixup 0
- contiguate 0
- junction 0
- MMseqs2 0
- InterProScan 0
- busco 0
- droplet based single cells 0
- antimicrobial reistance 0
- lexogen 0
- genotype-based demultiplexing 0
- donor deconvolution 0
- cellsnp 0
- trimfq 0
- bigbed 0
- cmseq 0
- bedtointervallist 0
- mash/sketch 0
- calibratedragstrmodel 0
- reduced 0
- representations 0
- getpileupsummaries 0
- cross-samplecontamination 0
- mass-spectroscopy 0
- calculatecontamination 0
- mcr-1 0
- MD5 0
- 128 bit 0
- taxonomic assignment 0
- asereadcounter 0
- daa 0
- rma6 0
- Neisseria meningitidis 0
- 3D heat map 0
- contour map 0
- Merqury 0
- annotateintervals 0
- targets 0
- cnnscorevariants 0
- collectreadcounts 0
- ploidy 0
- collapsing 0
- determinegermlinecontigploidy 0
- legionella 0
- clinical 0
- pneumophila 0
- createsomaticpanelofnormals 0
- limma 0
- Listeria monocytogenes 0
- createsequencedictionary 0
- condensedepthevidence 0
- lofreq/call 0
- lofreq/filter 0
- qualities 0
- estimate 0
- dragstr 0
- functional genomics 0
- sgRNA 0
- CRISPR-Cas9 0
- maximum-likelihood 0
- rra 0
- composestrtablefile 0
- short variant discovery 0
- combinegvcfs 0
- DNA damage 0
- NGS 0
- damage patterns 0
- collectsvevidence 0
- smudgeplot 0
- unionsum 0
- train 0
- graph drawing 0
- SNP table 0
- contaminant 0
- single molecule 0
- cancer genome 0
- somatic structural variations 0
- mobile element insertions 0
- sequencing summary 0
- NextGenMap 0
- ngm 0
- Neisseria gonorrhoeae 0
- gender 0
- zipperbams 0
- graph construction 0
- ubam 0
- Beautiful stand-alone HTML report 0
- squeeze 0
- odgi 0
- combine graphs 0
- graph stats 0
- graph unchopping 0
- graph formats 0
- graph viz 0
- tumor/normal 0
- hla-typing 0
- ILP 0
- HLA-I 0
- block-compressed 0
- unmapped 0
- GATK UnifiedGenotyper 0
- bioinformatics tools 0
- bootstrapping 0
- methylation bias 0
- mbias 0
- heattree 0
- gangstr 0
- assembler 0
- de Bruijn 0
- microrna 0
- gene-calling 0
- target prediction 0
- mitochondrial genome 0
- reference genome 0
- gamma 0
- UShER 0
- mosdepth 0
- mitochondrial to nuclear ratio 0
- bacterial variant calling 0
- germline variant calling 0
- somatic variant calling 0
- variant caller 0
- rust 0
- microsatellite instability 0
- fq 0
- lint 0
- random 0
- scan 0
- mtnucratio 0
- ratio 0
- generate 0
- adapter removal 0
- spliced 0
- flip 0
- txt 0
- abricate 0
- amrfinderplus 0
- fARGene 0
- rgi 0
- ibd 0
- hbd 0
- beagle 0
- mitochondrial 0
- genome profile 0
- Haemophilus influenzae 0
- haplotype resolution 0
- file parsing 0
- gawk 0
- extractvariants 0
- variantrecalibrator 0
- recalibration model 0
- variantfiltration 0
- svcluster 0
- svannotate 0
- gccounter 0
- splitintervals 0
- readcounter 0
- site depth 0
- HMMER 0
- amino acid 0
- shiftintervals 0
- compound 0
- extract_variants 0
- Hidden Markov Model 0
- gene model 0
- Haplotypes 0
- Imputation 0
- joint-variant-calling 0
- GNU 0
- merge compare 0
- genomes on a tree 0
- low coverage 0
- gget 0
- genome statistics 0
- genome manipulation 0
- genome summary 0
- tama_collapse.py 0
- gfastats 0
- TAMA 0
- gvcftools 0
- Mykrobe 0
- gstama/merge 0
- Salmonella Typhi 0
- repeat content 0
- gstama/polyacleanup 0
- genome heterozygosity 0
- genome size 0
- gunc 0
- gunzip 0
- models 0
- shiftfasta 0
- hmtnote 0
- reorder 0
- Klebsiella 0
- readorientationartifacts 0
- learnreadorientationmodel 0
- indexfeaturefile 0
- readcountssummary 0
- getpileupsumaries 0
- kallisto/index 0
- quant 0
- germlinevariantsites 0
- germlinecnvcaller 0
- germline contig ploidy 0
- digital normalization 0
- k-mer counting 0
- effective genome size 0
- pneumoniae 0
- jupytext 0
- panelofnormalscreation 0
- kegg 0
- kofamscan 0
- jointgenotyping 0
- genomicsdbimport 0
- genomicsdb 0
- gatherbqsrreports 0
- tranche filtering 0
- filtervarianttranches 0
- filterintervals 0
- estimatelibrarycomplexity 0
- duplication metrics 0
- papermill 0
- Jupyter 0
- annotations 0
- pixel_classification 0
- shiftchain 0
- pos 0
- haemophilus 0
- selectvariants 0
- revert 0
- panel_of_normals 0
- IDR 0
- igv 0
- igv.js 0
- js 0
- genome browser 0
- multicut 0
- pixel classification 0
- probability_maps 0
- Python 0
- reblockgvcf 0
- printsvevidence 0
- printreads 0
- interproscan 0
- preprocessintervals 0
- postprocessgermlinecnvcalls 0
- genomic islands 0
- insertion 0
- snvs 0
- mutectstats 0
- mergebamalignment 0
- leftalignandtrimvariants 0
- jasminesv 0
- jasmine 0
- PCR/optical duplicates 0
- upper-triangular matrix 0
- sequencing adapters 0
- custom 0
- sertotype 0
- interleave 0
- header 0
- seq 0
- na 0
- selection 0
- random draw 0
- pseudohaploid 0
- pseudodiploid 0
- freqsum 0
- bam2seqz 0
- induce 0
- sex determination 0
- sequence headers 0
- genetic sex 0
- relative coverage 0
- Cores 0
- Segmentation 0
- rare variants 0
- error 0
- TMA dearray 0
- de-novo 0
- longread 0
- sha256 0
- 256 bit 0
- UNet 0
- shinyngs 0
- cls 0
- grep 0
- boxplot 0
- scramble 0
- amplicon 0
- ampliconclip 0
- scatterplot 0
- corrrelation 0
- faidx 0
- track 0
- insert size 0
- repair 0
- paired 0
- read pairs 0
- readgroup 0
- paired-end 0
- cluster analysis 0
- subseq 0
- clusteridentifier 0
- pcr duplicates 0
- cutesv 0
- variant recalibration 0
- gct 0
- exploratory 0
- density 0
- sambamba 0
- rdtest2vcf 0
- spatype 0
- spa 0
- streptococcus 0
- sccmec 0
- variantcalling 0
- Sample 0
- protein coding genes 0
- detecting svs 0
- short-read sequencing 0
- polymorphic sites 0
- svtk/baftest 0
- baftest 0
- countsvtypes 0
- rdtest 0
- antitarget 0
- polymorphic 0
- vcf2bed 0
- decompress 0
- polymut 0
- polya tail 0
- fast5 0
- chromosome_visualization 0
- Mycobacterium tuberculosis 0
- chromosomal rearrangements 0
- eucaryotes 0
- coding 0
- cds 0
- transcroder 0
- access 0
- features 0
- cload 0
- mcool 0
- sliding window 0
- genomic bins 0
- makebins 0
- CRAM 0
- SMN1 0
- SMN2 0
- POA 0
- sniffles 0
- core 0
- snippy 0
- enzyme 0
- digest 0
- cooler/balance 0
- subcontigs 0
- dbnsfp 0
- predictions 0
- SNPs 0
- invariant 0
- constant 0
- partition histograms 0
- rRNA 0
- ribosomal RNA 0
- target 0
- export 0
- flagstat 0
- ligation junctions 0
- genetic 0
- deletions 0
- insertions 0
- tandem duplications 0
- CoPRO 0
- GRO-cap 0
- PRO-cap 0
- CAGE 0
- NETCAGE 0
- RAMPAGE 0
- csRNA-seq 0
- STRIPE-seq 0
- PRO-seq 0
- GRO-seq 0
- picard/renamesampleinvcf 0
- faqcs 0
- exclude 0
- variant identifiers 0
- str 0
- indep 0
- indep pairwise 0
- recode 0
- whole genome association 0
- identifiers 0
- scoring 0
- cache 0
- variant genetic 0
- sortvcf 0
- porechop_abi 0
- pbp 0
- pairtools 0
- pairstools 0
- restriction fragments 0
- select 0
- duplexumi 0
- public 0
- paragraph 0
- graphs 0
- pbbam 0
- pbmerge 0
- subreads 0
- pair-end 0
- liftovervcf 0
- read 0
- pedigrees 0
- ENA 0
- motif 0
- prophage 0
- identification 0
- SRA 0
- ANI 0
- hybrid-selection 0
- mate-pair 0
- pmdtools 0
- percent on target 0
- read distribution 0
- subsampling 0
- long uncorrected reads 0
- rhocall 0
- R 0
- escherichia coli 0
- bamstat 0
- depth information 0
- strandedness 0
- experiment 0
- read_pairs 0
- fragment_size 0
- inner_distance 0
- structural variation 0
- duphold 0
- PEP 0
- sequence-based 0
- mapping-based 0
- segment 0
- integrity 0
- rtg 0
- blastx 0
- pedfilter 0
- rocplot 0
- rtg-tools 0
- salsa 0
- salsa2 0
- neighbour-joining 0
- quast 0
- endogenous DNA 0
- circos 0
- Streptococcus pyogenes 0
- swissprot 0
- genbank 0
- contact 0
- pretext 0
- jpg 0
- bmp 0
- contact maps 0
- gene finding 0
- embl 0
- split by chromosome 0
- deletion 0
- genomic intervals 0
- schema 0
- normal database 0
- panel of normals 0
- cutoff 0
- eklipse 0
- haplotype purging 0
- duplicate purging 0
- false duplications 0
- assembly curation 0
- Haplotype purging 0
- eigenstratdatabasetools 0
- False duplications 0
- Assembly curation 0
- pep 0
- purging 0
- integron 0
No modules found..
Screen assemblies for antimicrobial resistance against multiple databases
010
report versions
Mass screening of contigs for antibiotic resistance genes
Screen assemblies for antimicrobial resistance against multiple databases
01
report versions
Mass screening of contigs for antibiotic resistance genes
A NATA accredited tool for reporting the presence of antimicrobial resistance genes in bacterial genomes
01
matches partials virulence out txt versions
A pipeline for running AMRfinderPlus and collating results into functional classes
Trim sequencing adapters and collapse overlapping reads
010
singles_truncated discarded paired_truncated collapsed collapsed_truncated paired_interleaved settings versions
Fixes prefixes from AdapterRemoval2 output to make sure no clashing read names are in the output. For use with DeDup.
01
fixed_fastq versions
ADMIXTURE is a program for estimating ancestry in a model-based manner from large autosomal SNP genotype datasets, where the individuals are unrelated (for example, the individuals in a case-control association study).
01230
ancestry_fractions allele_frequencies versions
Read CEL files into an ExpressionSet and generate a matrix
01201
rds expression annotation versions
Methods for Affymetrix Oligonucleotide Arrays
Takes a bed12 file and converts to a GFF3 file
01
gff versions
AGAT is a toolkit for manipulation and getting information from GFF/GTF files
Converts a GFF/GTF file into a proper GTF file
01
output_gtf log versions
AGAT is a toolkit for manipulation and getting information from GFF/GTF files
Converts a GFF/GTF file into a TSV file
01
tsv versions
AGAT is a toolkit for manipulation and getting information from GFF/GTF files
Fixes and standardizes GFF/GTF files and outputs a cleaned GFF/GTF file
01
output_gff log versions
AGAT is a toolkit for manipulation and getting information from GFF/GTF files
Add intron features to gtf/gff file without intron features.
010
gff versions
Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.
The script reads a gff annotation file, and create two output files, one contains the gene models with ORF passing the test, the other contains the rest. By default the test is "> 100" that means all gene models that have ORF longer than 100 Amino acids, will pass the test.
010
passed_gff failed_gff versions
Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.
The script aims to remove features based on a kill list. The default behaviour is to look at the features's ID. If the feature has an ID (case insensitive) listed among the kill list it will be removed. /!\ Removing a level1 or level2 feature will automatically remove all linked subfeatures, and removing all children of a feature will automatically remove this feature too.
0100
gff versions
Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.
The script flags the short introns with the attribute
010
gff versions
Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.
This script merge different gff annotation files in one. It uses the AGAT parser that takes care of duplicated names and fixes other oddities met in those files.
010
gff versions
Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.
Provides different type of statistics in text format from a GFF/GTF annotation file
01
stats_txt versions
AGAT is a toolkit for manipulation and getting information from GFF/GTF files
Provides basic statistics in text format from a GFF/GTF annotation file
01
stats_txt versions
AGAT is a toolkit for manipulation and getting information from GFF/GTF files
Rapid identification of Staphylococcus aureus agr locus type and agr operon variants
01
summary results_dir versions
Generates a count of coverage of alleles
01200
allelecount versions
A tool to parse and summarise results from antimicrobial peptides tools and present functional classification.
0100
sample_dir txt csv faa summary_csv summary_html log results_db results_db_dmnd results_db_fasta results_db_tsv versions
A submodule that clusters the merged AMP hits generated from ampcombi2/parsetables and ampcombi2/complete using MMseqs2 cluster.
0
cluster_tsv rep_cluster_tsv log versions
A tool for clustering all AMP hits found across many samples and supporting many AMP prediction tools.
A submodule that merges all output summary tables from ampcombi/parsetables in one summary file.
0
tsv log versions
This merges the per sample AMPcombi summaries generated by running 'ampcombi2/parsetables'.
A submodule that parses and standardizes the results from various antimicrobial peptide identification tools.
0100000
sample_dir contig_gbks db_tsv tsv faa sample_log full_log db db_txt db_fasta db_mmseqs versions
A parsing tool to convert and summarise the outputs from multiple AMP detection tools in a standardized format.
A fast and user-friendly method to predict antimicrobial peptides (AMPs) from any given size protein dataset. ampir uses a supervised statistical machine learning approach to predict AMPs.
01000
amps_faa amps_tsv versions
AMPlify is an attentive deep learning model for antimicrobial peptide prediction.
010
tsv versions
Attentive deep learning model for antimicrobial peptide prediction
Post-processing script of the MaltExtract component of the HOPS package
000
json summary_pdf tsv candidate_pdfs versions
Identify antimicrobial resistance in gene or protein sequences
010
report mutation_report versions tool_version db_version
AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences.
Identify antimicrobial resistance in gene or protein sequences
NO input
db versions
AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences.
A tool to estimate nuclear contamination in males based on heterozygosity in the female chromosome.
0101
txt versions
ANGSD: Analysis of next generation Sequencing Data
Calculates base frequency statistics across reference positions from BAM.
0123
depth_sample depth_global qs pos counts icounts versions
ANGSD: Analysis of next generation Sequencing Data
Calculated genotype likelihoods from BAM files.
010101
genotype_likelihood versions
ANGSD: Analysis of next generation Sequencing Data
Module to subset AnnData object to cells with matching barcodes from the csv file
012
h5ad versions
An annotated data matrix.
Get the size (n_cells or n_genes) of an anndata object stored as a h5ad file
010
size versions
An annotated data matrix.
Accelerating de novo SINE annotation in plant and animal genomes
010
log fa versions
Annotation and Ranking of Structural Variation
012301010101
tsv unannotated_tsv vcf versions
Annotation and Ranking of Structural Variation
Install the AnnotSV annotations
NO input
annotations versions
Annotation and Ranking of Structural Variation
Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq
0123012
translated_mrna total_mrna translation buffering mrna_abundance rdata fold_change_plot interaction_p_distribution_plot residual_distribution_summary_plot residual_vs_fitted_plot rvm_fit_for_all_contrasts_group_plot rvm_fit_for_interactions_plot rvm_fit_for_omnibus_group_plot simulated_vs_obt_dfbetas_without_interaction_plot session_info versions
Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq
antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters.
0100
clusterblast_file html_accessory_files knownclusterblast_html knownclusterblast_dir knownclusterblast_txt svg_files_clusterblast svg_files_knownclusterblast gbk_input json_results log zip gbk_results clusterblastoutput html knownclusterblastoutput json_sideloading versions
antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell
antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. This module downloads the antiSMASH databases for conda and docker/singularity runs.
000
database antismash_dir versions
antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell
Extracts reads mapped to chromosome 6 and any HLA decoys or chromosome 6 alternates.
01
extracted_reads_fastq log intermediate_sam intermediate_bam intermediate_sorted_bam versions
arcasHLA performs high resolution genotyping for HLA class I and class II genes from RNA sequencing, supporting both paired and single-end samples.
Normalize antibiotic resistance genes (ARGs) using the ARO ontology (developed by CARD).
0100
tsv versions
Download and prepare database for Ariba analysis
01
db versions
ARIBA: Antibiotic Resistance Identification By Assembly
Query input FASTQs against Ariba formatted databases
0101
results versions
ARIBA: Antibiotic Resistance Identification By Assembly
Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data.
0101010000
fusions fusions_fail versions
Fast and accurate gene fusion detection from RNA-Seq data
Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data.
0
blacklist cytobands protein_domains known_fusions versions
Fast and accurate gene fusion detection from RNA-Seq data
Simulation tool to generate synthetic Illumina next-generation sequencing reads
01000
fastq aln sam versions
ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles.
Aggregates fastq files with demultiplexed reads
01
fastq versions
ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore
Run the alignment/variant-call/consensus logic of the artic pipeline
01012012
results bam bai bam_trimmed bai_trimmed bam_primertrimmed bai_primertrimmed fasta vcf tbi json versions
ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore
copy number profiles of tumour cells.
01234000000
allelefreqs bafs cnvs logrs metrics png purityploidy segments versions
Alignment by Simultaneous Harmonization of Layer/Adjacency Registration
0100
tif versions
Assembly summary statistics in JSON format
01
json versions
ataqv function of a corresponding ataqv tool
012300000
json problems versions
ataqv is a toolkit for measuring and comparing ATAC-seq results. It was written to help understand how well ATAC-seq assays have worked, and to make it easier to spot differences that might be caused by library prep or sequencing.
mkarv function of a corresponding ataqv tool
0
html versions
ataqv is a toolkit for measuring and comparing ATAC-seq results. It was written to help understand how well ATAC-seq assays have worked, and to make it easier to spot differences that might be caused by library prep or sequencing.
generate VCF file from a BAM file using various calling methods
012340000
vcf versions
ATLAS, a suite of methods to accurately genotype and estimate genetic diversity
Estimate the post-mortem damage patterns of DNA
012300
empiric exponential counts table versions
ATLAS, a suite of methods to accurately genotype and estimate genetic diversity
Gives an estimation of the sequencing bias based on known invariant sites
0123400
recal_patterns versions
ATLAS, a suite of methods to accurately genotype and estimate genetic diversity
split single end read groups by length and merge paired end reads
01234
bam txt versions
ATLAS, a suite of methods to accurately genotype and estimate genetic diversity
Generate tables of feature metadata from GTF files
0101
feature_annotation filtered_cdna versions
Scripts for manipulating gene annotation
Use deamination patterns to estimate contamination in single-stranded libraries
010101
txt versions
Estimates present-day DNA contamination in ancient DNA single-stranded libraries.
Pixel-by-pixel channel subtraction scaled by exposure times of pre-stitched tif images.
0101
backsub_tif markerout versions
Annotation of bacterial genomes (isolates, MAGs) and plasmids
01000
embl faa ffn fna gbff gff hypotheticals_tsv hypotheticals_faa tsv txt versions
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids.
Downloads BAKTA database from Zenodo
NO input
db versions
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
Conversion of PacBio BAM files into gzipped fastq files, including splitting of barcoded data
012
fastq versions
Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files
removes unused references from header of sorted BAM/CRAM files.
01
bam versions
This module is used to clip primer sequences from your alignments.
0123
bam bai versions
Bamcmp (Bam Compare) is a tool for assigning reads between a primary genome and a contamination genome. For instance, filtering out mouse reads from patient derived xenograft mouse models (PDX).
012
primary_filtered_bam contamination_bam versions
write your description here
01
json versions
A command line tool to compute mapping statistics from a BAM file
Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis
01
fastq versions
BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
01
bam versions
C++ API & command-line toolkit for working with BAM data
BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
01
stats versions
C++ API & command-line toolkit for working with BAM data
Render an assembly graph in GFA 1.0 format to PNG and SVG image formats
01
png svg versions
Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
Demultiplex Element Biosciences bases files
012
sample_fastq sample_json qc_report run_stats generated_run_manifest metrics unassigned versions
BaSiCPy is a python package for background and shading correction of optical microscopy images. It is developed based on the Matlab version of BaSiC tool with major improvements in the algorithm.
01
profiles versions
Adapter and quality trimming of sequencing reads
010
reads log versions
BBMap is a short read aligner, as well as various other bioinformatic tools.
Merging overlapping paired reads into a single read.
010
merged unmerged ihist versions log
BBMap is a short read aligner, as well as various other bioinformatic tools.
BBNorm is designed to normalize coverage by down-sampling reads over high-depth areas of a genome, to result in a flat coverage distribution.
01
fastq log versions
BBMap is a short read aligner, as well as various other bioinformatic tools.
Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates
01
reads log versions
BBMap is a short read aligner, as well as various other bioinformatic tools.
Filter out sequences by sequence header name(s)
01000
reads log versions
BBMap is a short read aligner, as well as various other bioinformatic tools.
Creates an index from a fasta file, ready to be used by bbmap.sh in mapping mode.
0
index versions
BBMap is a short read aligner, as well as various other bioinformatic tools.
Calculates per-scaffold or per-base coverage information from an unsorted sam or bam file.
01
covstats hist versions
BBMap is a short read aligner, as well as various other bioinformatic tools.
Re-pairs reads that became disordered or had some mates eliminated.
010
repaired singleton versions log
Repair.sh is a tool that re-pairs reads that became disordered or had some mates eliminated tools.
Compares query sketches to reference sketches hosted on a remote server via the Internet.
01
hits versions
BBMap is a short read aligner, as well as various other bioinformatic tools.
This command replaces the former bcftools view caller. Some of the original functionality has been temporarily lost in the process of transition under htslib, but will be added back on popular demand. The original calling model can be invoked with the -c option.
012000
vcf tbi csi versions
View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
Concatenate VCF files
012
vcf tbi csi versions
Concatenate VCF files.
Compresses VCF files
01234
fasta versions
Create consensus sequence by applying VCF variants to a reference fasta file.
Converts certain output formats to VCF
012010
vcf_gz vcf bcf_gz bcf hap legend samples tbi csi versions
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
bcftools Haplotype-aware consequence caller
01010101
vcf tbi csi versions
Haplotype-aware consequence caller
Filters VCF files
012
vcf tbi csi versions
Apply fixed-threshold filters to VCF files.
Index VCF tools
01
csi tbi versions
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
Apply set operations to VCF files
012
results versions
Computes intersections, unions and complements of VCF files.
Merge VCF files
012010101
vcf index versions
Merge VCF files.
Compresses VCF files
012010
vcf tbi stats mpileup versions
Generates genotype likelihoods at each genomic position with coverage.
Normalize VCF file
01201
vcf tbi csi versions
Normalize VCF files.
Adds imputation information metrics to the INFO field based on selected FORMAT tags. Only the IMPUTE2 INFO metric from FORMAT/GP tags is currently available.
01200
vcf tbi csi versions
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
Bcftools plugins are tools that can be used with bcftools to manipulate variant calls in Variant Call Format (VCF) and BCF. The impute-info plugin adds imputation information metrics to the INFO field based on selected FORMAT tags. Only the IMPUTE2 INFO metric from FORMAT/GP tags is currently available
Split VCF by chunks or regions, creating multiple VCFs.
01200000
scatter tbi csi versions
Split VCF by chunks or regions, creating multiple VCFs.
Sets genotypes according to the specified criteria and filtering expressions. For example, missing genotypes can be set to ref, but much more than that.
0120000
vcf tbi csi versions
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
Bcftools plugins are tools that can be used with bcftools to manipulate variant calls in Variant Call Format (VCF) and BCF. The setGT plugin sets genotypes according to the specified criteria and filtering expressions. For example, missing genotypes can be set to ref, but much more than that.
Split VCF by sample, creating single- or multi-sample VCFs.
0120000
vcf tbi csi versions
Split VCF by sample, creating single- or multi-sample VCFs.
Converts between similar tags, such as GL,PL,GP or QR,QA,QS or localized alleles, eg LPL,LAD.
01200
vcf tbi csi versions
Converts between similar tags, such as GL,PL,GP or QR,QA,QS or localized alleles, eg LPL,LAD.
Extracts fields from VCF or BCF files and outputs them in user-defined format.
012000
output versions
Extracts fields from VCF or BCF files and outputs them in user-defined format.
Reheader a VCF file
012301
vcf index versions
Modify header of VCF/BCF files, change sample names.
A program for detecting runs of homo/autozygosity. Only bi-allelic sites are considered.
012010000
roh versions
A program for detecting runs of homo/autozygosity. Only bi-allelic sites are considered.
Sorts VCF files
01
vcf tbi csi versions
Sort VCF files by coordinates.
Split a vcf file into files per chromosome
012
split_vcf versions
Sort VCF files by coordinates.
Generates stats from VCF files
0120101010101
stats versions
Parses VCF or BCF and produces text file stats which is suitable for machine processing and can be plotted using plot-vcfstats.
View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
012000
vcf tbi csi versions
View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
Demultiplex Illumina BCL files
012
fastq fastq_idx undetermined undetermined_idx reports stats interop versions
Demultiplex Illumina BCL files
012
fastq fastq_idx undetermined undetermined_idx reports logs interop versions
Beagle v5.2 is a software package for phasing genotypes and for imputing ungenotyped markers.
010000
vcf log versions
Beagle is a software package for phasing genotypes and for imputing ungenotyped markers.
Convert a BED file to a VCF file according to a YAML config
01201
vcf versions
Convert BAM/GFF/GTF/GVF/PSL files to bed
01
bed versions
High-performance genomic feature operations.
Convert gtf format to bed format
01
bed versions
The gtf2bed script converts 1-based, closed [start, end] Gene Transfer Format v2.2 (GTF2.2) to sorted, 0-based, half-open [start-1, end) extended BED-formatted data.
Returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file.
010
bed versions
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences) for a given genome.
012000
genomecov versions
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
extract sequences in a FASTA file based on intervals defined in a feature file.
010
fasta versions
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
Groups features in a BED file by given column(s) and computes summary statistics for each group to another column.
010
bed versions
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
Allows one to screen for overlaps between two sets of genomic features.
01201
intersect versions
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
Calculate Jaccard statistic b/w two feature files.
01201
tsv versions
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
Makes adjacent or sliding windows across a genome or BED file.
01
bed versions
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
masks sequences in a FASTA file based on intervals defined in a feature file.
010
fasta versions
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
combines overlapping or โbook-endedโ features in an interval file into a single feature which spans all of the combined features.
01
bed versions
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
Identifies common intervals among multiple (and subsets thereof) sorted BED/GFF/VCF files.
010
bed versions
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
Profiles the nucleotide content of intervals in a fasta file.
012
bed versions
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
bedtools shuffle will randomly permute the genomic locations of a feature file among a genome defined in a genome file
010100
bed versions
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
Adds a specified number of bases in each direction (unique values may be specified for either -l or -r)
010
bed versions
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
Sorts a feature file by chromosome and other criteria.
010
sorted versions
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
Split BED files into several smaller BED files
012
beds versions
A powerful toolset for genome arithmetic
Finds overlaps between two sets of regions (A and B), removes the overlaps from A and reports the remaining portion of A.
012
bed versions
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
Combines multiple BedGraph files into a single file
0101
bed versions
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
Locate and tag duplicate reads in a BAM file
01
bam metrics versions
biobambam is a set of tools for early stage alignment file processing.
Merge a list of sorted bam files
01
bam bam_index checksum versions
biobambam is a set of tools for early stage alignment file processing.
Parallel sorting and duplicate marking
0101
bam bam_index cram metrics versions
biobambam is a set of tools for early stage alignment file processing.
Use k-mers to rapidly subtype S. enterica genomes
010
summary kmer_results simple_summary versions
Aligns single- or paired-end reads from bisulfite-converted libraries to a reference genome using Biscuit.
010101
bam bai versions
A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
A fast, compact one-liner to produce duplicate-marked, sorted, and indexed BAM files using Biscuit
010101
bam bai versions
A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
samblaster is a fast and flexible program for marking duplicates in read-id grouped paired-end SAM files. It can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. By default, samblaster reads SAM input from stdin and writes SAM to stdout.
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
Summarize and/or filter reads based on bisulfite conversion rate
01010101
bam versions
A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
Summarizes read-level methylation (and optionally SNV) information from a Biscuit BAM file in a standard-compliant BED format.
0101010101
bed versions
A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
Indexes a reference genome for use with Biscuit
01
index versions
A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
Merges methylation information for opposite-strand C's in a CpG context
010101
bed versions
A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
Computes cytosine methylation and callable SNV mutations, optionally in reference to a germline BAM to call somatic variants
012340101
vcf versions
A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
Perform basic quality control on a BAM file generated with Biscuit
010101
reports versions
A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
Summarizes methylation or SNV information from a Biscuit VCF in a standard-compliant BED file.
01
bed versions
A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
Performs alignment of BS-Seq reads using bismark
010101
bam report unmapped versions
Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.
Relates methylation calls back to genomic cytosine contexts.
010101
coverage report summary versions
Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.
Removes alignments to the same position in the genome from the Bismark mapping output.
01
bam report versions
Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.
Converts a specified reference genome into two different bisulfite converted versions and indexes them for alignments.
01
index versions
Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.
Extracts methylation information for individual cytosines from alignments.
0101
bedgraph methylation_calls coverage report mbias versions
Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.
Collects bismark alignment reports
01234
report versions
Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.
Uses Bismark report files of several samples in a run folder to generate a graphical summary HTML report.
00000
summary versions
Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.
Retrieve entries from a BLAST database
01201
fasta text versions
BLAST finds regions of similarity between biological sequences.
Queries a BLAST DNA database
0101
txt versions
BLAST finds regions of similarity between biological sequences.
BLASTP (Basic Local Alignment Search Tool- Protein) compares an amino acid (protein) query sequence against a protein database
01010
xml tsv csv versions
BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit.
Builds a BLAST database
01
db versions
BLAST finds regions of similarity between biological sequences.
Queries a BLAST DNA database
0101
txt versions
Protein to Translated Nucleotide BLAST.
Downloads a BLAST database from NCBI
01
db versions
BLAST finds regions of similarity between biological sequences.
Create bowtie index for reference genome
01
index versions
bowtie is a software package for mapping DNA sequences against a large reference genome, such as the human genome.
Re-estimate taxonomic abundance of metagenomic samples analyzed by kraken.
010
reports txt versions
Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
Extends a Kraken2 database to be compatible with Bracken
01
db bracken_files versions
Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
Combine output of metagenomic samples analyzed by bracken.
01
txt versions
Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
Benchmarking Universal Single Copy Orthologs
metafastamodelineagebusco_lineages_pathconfig_file
meta batch_summary short_summaries_txt short_summaries_json busco_dir full_table missing_busco_list single_copy_proteins seq_dir translated_proteins versions
Benchmarking Universal Single Copy Orthologs
0100000
batch_summary short_summaries_txt short_summaries_json log full_table missing_busco_list single_copy_proteins seq_dir translated_dir busco_dir downloaded_lineages single_copy_faa single_copy_fna versions
BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB.
Download database for BUSCO
0
download_dir versions
BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB.
BUSCO plot generation tool
0
png versions
BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB.
Construct species phylogenies using BUSCO proteins
01
gene_trees supermatrix versions
Construct species phylogenies using BUSCO proteins
Create BWA-mem2 index for reference genome
01
index versions
BWA-mem2 is a software package for mapping DNA sequences against a large reference genome, such as the human genome.
Create BWA-MEME index for reference genome
01
index versions
Faster BWA-MEM2 using learned-index
Performs alignment of BS-Seq reads using bwameth
010101
bam versions
Fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome.
Performs indexing of c2t converted reference genome
01
index versions
Fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome.
A module for concatenation of gzipped or uncompressed files
01
file_out versions
Just concatenation
Concatenates fastq files
01
reads versions
The cat utility reads files sequentially, writing them to the standard output.
Taxonomic classification of long DNA sequences and metagenome assembled genomes (e.g. MAGs / bins).
0101
txt versions
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
Taxonomic classification of long DNA sequences and metagenome assembled genomes (e.g. MAGs / bins).
0101010101
orf2lca bin2classification log diamond faa gff versions
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
Taxonomic classification of long DNA sequences and metagenome assembled genomes (e.g. contigs, MAGs / bins).
0101010101
orf2lca contig2classification log diamond faa gff versions
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
Downloads the required files for either Nr or GTDB for building into a CAT database
01
rawdb versions
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
Taxonomic classification plus read-based abundance estimation from long DNA sequences and metagenome assembled genomes (e.g. contigs, MAGs / bins).
0101010101001010101010101
rat_log complete_abundance contig_abundance read2classification alignment_diamond contig2classification cat_log orf2lca faa gff unmapped_diamond unmapped_fasta unmapped2classification versions
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
Summarises results from CAT/BAT/RAT classification steps
0101
txt versions
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
Cluster protein sequences using sequence similarity
01
fasta clusters versions
Clusters and compares protein or nucleotide sequences
Cluster nucleotide sequences using sequence similarity
01
fasta clusters versions
Clusters and compares protein or nucleotide sequences
Unsupervised machine learning for cell type identification in multiplexed imaging using protein expression and cell neighborhood information without ground truth
01000
celltypes quality versions
Module to use CellBender to remove ambient RNA from single-cell RNA-seq data
0123
h5ad versions
CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
Module to use CellBender to estimate ambient RNA from single-cell RNA-seq data
01
h5 filtered_h5 posterior_h5 barcodes metrics report pdf log checkpoint versions
CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
Module to use Cell Ranger's pipelines analyze sequencing data produced from Chromium Single Cell Gene Expression.
010
outs versions
Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
Module to create FASTQs needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkfastq command.
012
fastq undetermined_fastq reports stats interop versions
Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
Module to build a filtered GTF needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkgtf command.
0
gtf versions
Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
Module to build the reference needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkref command.
000
reference versions
Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
Module to build the VDJ reference needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkvdjref command.
0000
reference versions
Cell Ranger processes data from 10X Genomics Chromium kits. cellranger vdj takes FASTQ files from cellranger mkfastq or bcl2fastq for V(D)J libraries and performs sequence assembly and paired clonotype calling. It uses the Chromium cellular barcodes and UMIs to assemble V(D)J transcripts per cell. Clonotypes and CDR3 sequences are output as a .vloupe file which can be loaded into Loupe V(D)J Browser.
Module to use Cell Ranger's pipelines to analyze sequencing data produced from various Chromium technologies, including Single Cell Gene Expression, Single Cell Immune Profiling, Feature Barcoding, and Cell Multiplexing.
00101010101010000000000000
config outs versions
Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
Module to use Cell Ranger's pipelines analyze sequencing data produced from Chromium Single Cell Immune Profiling.
010
outs versions
Cell Ranger processes data from 10X Genomics Chromium kits. cellranger vdj takes FASTQ files from cellranger mkfastq or bcl2fastq for V(D)J libraries and performs sequence assembly and paired clonotype calling. It uses the Chromium cellular barcodes and UMIs to assemble V(D)J transcripts per cell. Clonotypes and CDR3 sequences are output as a .vloupe file which can be loaded into Loupe V(D)J Browser.
Module to use Cell Ranger's ARC pipelines analyze sequencing data produced from Chromium Single Cell ARC. Uses the cellranger-arc count command.
01230
outs lib versions
Cell Ranger ARC is a set of analysis pipelines that process Chromium Single Cell ARC data.
Module to create fastqs needed by the 10x Genomics Cell Ranger Arc tool. Uses the cellranger-arc mkfastq command.
00
versions fastq
Cell Ranger Arc by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
Module to build a filtered gtf needed by the 10x Genomics Cell Ranger Arc tool. Uses the cellranger-arc mkgtf command.
0
gtf versions
Cell Ranger Arc by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
Module to build the reference needed by the 10x Genomics Cell Ranger Arc tool. Uses the cellranger-arc mkref command.
00000
reference config versions
Cell Ranger Arc is a set of analysis pipelines that process Chromium Single Cell Arc data.
Module to use Cell Ranger's ATAC pipelines analyze sequencing data produced from Chromium Single Cell ATAC.
010
outs versions
Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data.
Module to create fastqs needed by the 10x Genomics Cell Ranger ATAC tool. Uses the cellranger-atac mkfastq command.
00
versions fastq
Cell Ranger ATAC by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
Module to build the reference needed by the 10x Genomics Cell Ranger ATAC tool. Uses the cellranger-atac mkref command.
00000
reference versions
Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data.
Cellsnp-lite is a C/C++ tool for efficient genotyping bi-allelic SNPs on single cells. You can use the mode A of cellsnp-lite after read alignment to obtain the snp x cell pileup UMI or read count matrices for each alleles of given or detected SNPs for droplet based single cell data.
01234
base cell sample allele_depth depth_coverage depth_other versions
Efficient genotyping bi-allelic SNPs on single cells
Build centrifuge database for taxonomic profiling
010000
cf versions
Classifier for metagenomic sequences
Classifies metagenomic sequence data
01000
report results sam fastq_mapped fastq_unmapped versions
Centrifuge is a classifier for metagenomic sequences.
Creates Kraken-style reports from centrifuge out files
010
kreport versions
Centrifuge is a classifier for metagenomic sequences.
CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.
0100
checkm_output marker_file checkm_tsv versions
Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.
01230
output fasta versions
Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
CheckM2 database download
0
database versions
CheckM2 - Rapid assessment of genome bin quality using machine learning
CheckM2 bin quality prediction
0101
checkm2_output checkm2_tsv versions
CheckM2 - Rapid assessment of genome bin quality using machine learning
Construct the database necessary for checkv's quality assessment
NO input
checkv_db versions
Assess the quality of metagenome-assembled viral genomes.
Assess the quality of metagenome-assembled viral genomes.
010
quality_summary completeness contamination complete_genomes proviruses viruses versions
Assess the quality of metagenome-assembled viral genomes.
Construct the database necessary for checkv's quality assessment
010
checkv_db versions
Assess the quality of metagenome-assembled viral genomes.
Determine the allelic profiles of a genome using a pre-defined schema
0101
stats contigs_info alleles log paralogous_counts paralogous_loci cds_coordinates invalid_cds loci_summary_stats versions
A complete suite for gene-by-gene schema creation and strain identification.
Create a schema to determine the allelic profiles of a genome
0100
schema cds_coordinates invalid_cds versions
A complete suite for gene-by-gene schema creation and strain identification.
Filter and trim long read data.
010
fastq versions
zcat uncompresses either a list of files on the command line or its standard input and writes the uncompressed data on standard output.
Gzip reduces the size of the named files using Lempel-Ziv coding (LZ77).
Performs preprocessing and alignment of chromatin fastq files to fasta reference files using chromap.
0101010000
bed bam tagAlign pairs versions
Fast alignment and preprocessing of chromatin profiles
Indexes a fasta reference genome ready for chromatin profiling.
01
index versions
Fast alignment and preprocessing of chromatin profiles
Chromograph is a python package to create PNG images from genetics data such as BED and WIG files.
01010101010101
plots versions
Annotate circRNAs detected in the output from CIRCexplorer2 parse
0100
txt versions
Circular RNA analysis toolkits
CIRCexplorer2 parses fusion junction files from multiple aligners to prepare them for CIRCexplorer2 annotate.
01
junction versions
Circular RNA analysis toolkit
A method to improve mappings on circular genomes, using the BWA mapper.
010101
fasta elongated versions
Creating a modified reference genome, with an elongation of the an specified amount of bases
Realign reads mapped with BWA to elongated reference genome
01010101
bam versions
A method to improve mappings on circular genomes such as Mitochondria.
Predict recomination events in bacterial genomes
012
emsim em status newick fasta pos_ref versions
Align sequences using Clustal Omega
010100000
alignment versions
Latest version of Clustal: a multiple sequence alignment program for DNA or proteins
Parallel implementation of the gzip algorithm.
Renders a guidetree in clustalo
01
tree versions
Latest version of Clustal: a multiple sequence alignment program for DNA or proteins
Calculates polymorphic site rates over protein coding genes
01234
polymut versions
Set of utilities on sequences and BAM files
Calculate the sequence-accessible coordinates in chromosomes from the given reference genome, output as a BED file.
0101
bed versions
CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.
Derive off-target (โantitargetโ) bins from target regions.
01
bed versions
CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.
Copy number variant detection from high-throughput sequencing data
012010101010
bed cnn cnr cns pdf png versions
CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.
Given segmented log2 ratio estimates (.cns), derive each segmentโs absolute integer copy number
012
cns versions
CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.
Convert copy number ratio tables (.cnr files) or segments (.cns) to another format.
01
output versions
CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.
Copy number variant detection from high-throughput sequencing data
012
tsv cnn versions
CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.
Compile a coverage reference from the given files (normal samples).
000
cnn versions
CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.
Transform bait intervals into targets more suitable for CNVkit.
0101
bed versions
CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.
CNVnator is a command line tool for CNV/CNA analysis from depth-of-coverage by mapped reads.
012010101
root tab versions
Tool for calling copy number variations.
convert2vcf.pl is command line tool to convert CNVnator calls to vcf format.
01
vcf versions
Tool for calling copy number variations.
Command line tool for calling CNVs in whole genome sequencing data
010
pytor versions
calling CNVs using read depth
calculates read depth histograms
010
pytor versions
calling CNVs using read depth
command line tool for CNV/CNA analysis. This step imports the read depth data into a root pytor file.
01200
pytor versions
calling CNVs using read depth
partitioning read depth histograms
010
pytor versions
calling CNVs using read depth
view function to generate vcfs
0100
vcf tsv xls versions
calling CNVs using read depth
A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.
01010101000
self_circular extended_circular extended_partial extended_failed orphan_end all_cobra_assemblies joining_summary log versions
COBRA is a tool to get higher quality viral genomes assembled from metagenomes.
Builds a classic bloom filter COBS index
01
index versions
Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)
Builds a compact bloom filter COBS index
01
index versions
Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)
Unsupervised binning of metagenomic contigs by using nucleotide composition - kmer frequencies - and coverage data for multiple samples
012
args_txt clustering_csv log_txt original_data_csv pca_components_csv pca_transformed_csv versions
Clustering cONtigs with COverage and ComposiTion
Generate the input coverage table for CONCOCT using a BEDFile
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tsv versions
Clustering cONtigs with COverage and ComposiTion
Calculate confidence scores from Kraken2 output
010
score versions
Add both Wilcoxon test and Kolmogorov-Smirnov test p-values to each CNV output of FREEC
012
p_value_txt versions
Copy number and genotype annotation from whole genome and whole exome sequencing data.
Copy number and genotype annotation from whole genome and whole exome sequencing data
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bedgraph control_cpn sample_cpn gcprofile_cpn BAF CNV info ratio config versions
Copy number and genotype annotation from whole genome and whole exome sequencing data.
Plot Freec output
01
bed versions
Copy number and genotype annotation from whole genome and whole exome sequencing data.
Format Freec output to circos input format
01
circos versions
Copy number and genotype annotation from whole genome and whole exome sequencing data.
Plot Freec output
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png_baf png_ratio_log2 png_ratio versions
Copy number and genotype annotation from whole genome and whole exome sequencing data.
Plot Freec output
012
png_baf png_ratio_log2 png_ratio versions
Copy number and genotype annotation from whole genome and whole exome sequencing data.
Run matrix balancing on a cool file
012
cool versions
Sparse binary format for genomic interaction matrices
Create a cooler from genomic pairs and bins
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cool versions
Sparse binary format for genomic interaction matrices
Generate fragment-delimited genomic bins
000
bed versions
Sparse binary format for genomic interaction matrices
Dump a coolerโs data to a text stream.
012
bedpe versions
Sparse binary format for genomic interaction matrices
Generate fixed-width genomic bins
012
bed versions
Sparse binary format for genomic interaction matrices
Merge multiple coolers with identical axes
01
cool versions
Sparse binary format for genomic interaction matrices
Generate a multi-resolution cooler file by coarsening
01
mcool versions
Sparse binary format for genomic interaction matrices
Calculates peak-to-through ratio (PTR) from metagenomic sequence data
01
ptr versions
Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reads.
Computes the coverage map along the reference genome
01
coverage versions
Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reads.
Indexes a directory of fasta files for use with CoPTR
01
index_dir versions
Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reads.
Merge reads that were mapped to multiple indices
01
bam versions
Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reads.
Great....yet another TMA dearray program. What does this one do? Coreograph uses UNet, a deep learning model, to identify complete/incomplete tissue cores on a tissue microarray. It has been trained on 9 TMA slides of different sizes and tissue types.
01
cores masks tma_map centroids versions
Map reads to contigs and estimate coverage
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coverage versions
CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications
Compress files with crabz
01
archive versions
Like pigz, but rust
Decompress files with crabz
01
file versions
Like pigz, but rust
remove false positives of functional crispr genomics due to CNVs
01200
norm_count_file versions
Analysis of CRISPR functional genomics, remove false positive due to CNVs.
Concatenate two or more CSV (or TSV) tables into a single table
0100
csv versions
A cross-platform, efficient, practical CSV/TSV toolkit
Join two or more CSV (or TSV) tables by selected fields into a single table
01
csv versions
A cross-platform, efficient, practical CSV/TSV toolkit
Splits CSV/TSV into multiple files according to column values
0100
split_csv versions
CSVTK is a cross-platform, efficient and practical CSV/TSV toolkit that allows rapid data investigation and manipulation.
Annotate a VEP annotated VCF with the most severe consequence field
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vcf versions
Custom module to annotate a VEP annotated VCF with the most severe consequence field
Annotate a VEP annotated VCF with the most severe pLi field
01
vcf versions
Custom module to annotate a VEP annotated VCF with the most severe pLi field
Custom module to Add a new fasta file to an old one and update an associated GTF
012010
fasta gtf versions
Custom module to Add a new fasta file to an old one and update an associated GTF
Custom module used to dump software versions within the nf-core pipeline template
0
yml mqc_yml versions
Custom module used to dump software versions within the nf-core pipeline template
Filters a differential expression table based on logFC and adjusted p-value thresholds
01012012
filtered versions
Python library for data manipulation and analysis
Generates a FASTA file of chromosome sizes and a fasta index file
01
sizes fai gzi versions
Tools for dealing with SAM, BAM and CRAM files
Filter a gtf file to keep only regions that are located on a chromosome represented in a given fasta file
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gtf versions
Filter a gtf file to keep only regions that are located on a chromosome represented in a given fasta file
filter a matrix based on a minimum value and numbers of samples that must pass.
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filtered tests session_info versions
filter a matrix based on a minimum value and numbers of samples
Test for the presence of suitable NCBI settings or create them on the fly.
0
ncbi_settings versions
SRA Toolkit and SDK from NCBI
Make a GSEA class file (.chip) from tabular inputs
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chip versions
Make a GSEA annotation file (.chip) from tabular inputs
Make a GSEA class file (.cls) from tabular inputs
01
cls versions
Make a GSEA class file (.cls) from tabular inputs
Convert a TSV or CSV with features by row and observations by column to a GCT format file as consumed by GSEA
01
gct versions
Convert a TSV or CSV with features by row and observations by column to a GCT format file as consumed by GSEA
Make a transcript/gene mapping from a GTF and cross-reference with transcript quantifications.
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tx2gene versions
"Custom module to create a transcript to gene mapping from a GTF and check it against transcript quantifications"
Perform adapter/quality trimming on sequencing reads
01
reads log versions
Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
structural-variant calling with cutesv
01201
vcf versions
A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage
01000
results versions
DAS Tool binning step.
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log summary contig2bin eval bins pdfs fasta_proteins candidates_faa fasta_archaea_scg fasta_bacteria_scg b6 seqlength versions
DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.
Helper script to convert a set of bins in fasta format to tabular scaffolds2bin format
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fastatocontig2bin versions
DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.
Helper script to convert a set of bins in fasta format to tabular scaffolds2bin format
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scaffolds2bin versions
DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.
Datavzrd is a tool to create visual HTML reports from collections of CSV/TSV tables.
0
report versions
decoupler is a package containing different statistical methods to extract biological activities from omics data within a unified framework. It allows to flexibly test any enrichment method with any prior knowledge resource and incorporates methods that take into account the sign and weight. It can be used with any omic, as long as its features can be linked to a biological process based on prior knowledge. For example, in transcriptomics gene sets regulated by a transcription factor, or in phospho-proteomics phosphosites that are targeted by a kinase.
0100
dc_estimate dc_pvals versions
DeDup is a tool for read deduplication in paired-end read merging (e.g. for ancient DNA experiments).
01
bam json hist log versions
A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes
NO input
db versions
A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes
A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes
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daa daa_tsv arg potential_arg versions
A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes
Database download module for DeepBGC which detects BGCs in bacterial and fungal genomes using deep learning.
NO input
db versions
DeepBGC - Biosynthetic Gene Cluster detection and classification
DeepBGC detects BGCs in bacterial and fungal genomes using deep learning.
010
readme log json bgc_gbk bgc_tsv full_gbk pfam_tsv bgc_png pr_png roc_png score_png versions
DeepBGC - Biosynthetic Gene Cluster detection and classification
Deepcell/mesmer segmentation for whole-cell
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mask versions
Deep cell is a collection of tools to segment imaging data
DeepSomatic is an extension of deep learning-based variant caller DeepVariant that takes aligned reads (in BAM or CRAM format) from tumor and normal data, produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports somatic variants in a standard VCF or gVCF file.
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vcf vcf_tbi gvcf gvcf_tbi versions
A Deep Learning Model for Transmembrane Topology Prediction and Classification
01
gff3 line3 md csv png versions
This tool filters alignments in a BAM/CRAM file according the the specified parameters.
012
bam logs versions
A set of user-friendly tools for normalization and visualization of deep-sequencing data
This tool takes an alignment of reads or fragments as input (BAM file) and generates a coverage track (bigWig or bedGraph) as output.
01200
bigwig bedgraph versions
A set of user-friendly tools for normalization and visualization of deep-sequencing data
calculates scores per genome regions for other deeptools plotting utilities
010
matrix table versions
A set of user-friendly tools for normalization and visualization of deep-sequencing data
Computes read coverage for genomic regions (bins) across the entire genome.
0123
matrix versions
A set of user-friendly tools for normalization and visualization of deep-sequencing data
Visualises sample correlations using a compressed matrix generated by mutlibamsummary or multibigwigsummary as input.
0100
pdf matrix versions
A set of user-friendly tools for normalization and visualization of deep-sequencing data
plots cumulative reads coverages by BAM file
012
pdf matrix metrics versions
A set of user-friendly tools for normalization and visualization of deep-sequencing data
plots values produced by deeptools_computematrix as a heatmap
01
pdf table versions
A set of user-friendly tools for normalization and visualization of deep-sequencing data
Generates principal component analysis (PCA) plot using a compressed matrix generated by multibamsummary or multibigwigsummary as input.
01
pdf tab versions
A set of user-friendly tools for normalization and visualization of deep-sequencing data
plots values produced by deeptools_computematrix as a profile plot
01
pdf table versions
A set of user-friendly tools for normalization and visualization of deep-sequencing data
(DEPRECATED - see main.nf) DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
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vcf vcf_tbi gvcf gvcf_tbi versions
Call variants from the examples produced by make_examples
01
call_variants_tfrecords versions
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
Transforms the input alignments to a format suitable for the deep neural network variant caller
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examples gvcf small_model_calls versions
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
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vcf vcf_index gvcf gvcf_index versions
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
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vcf vcf_tbi gvcf gvcf_tbi versions
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
01
report versions
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
Call structural variants
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bcf csi versions
Structural variant discovery by integrated paired-end and split-read analysis
Demultiplexing cell nucleus hashing data, using the estimated antibody background probability.
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zarr out_zarr versions
runs a differential expression analysis with DESeq2
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results dispersion_plot rdata size_factors normalised_counts rlog_counts vst_counts model session_info versions
Differential gene expression analysis based on the negative binomial distribution
Queries a DIAMOND database using blastp mode
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blast xml txt daa sam tsv paf versions
Accelerated BLAST compatible local sequence aligner
Queries a DIAMOND database using blastx mode
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blast xml txt daa sam tsv paf log versions
Accelerated BLAST compatible local sequence aligner
calculate clusters of highly similar sequences
01
tsv versions
Accelerated BLAST compatible local sequence aligner
Builds a DIAMOND database
01000
db versions
Accelerated BLAST compatible local sequence aligner
Doublet detection in single-cell RNA-seq data
01
h5ad predictions versions
Create DRAGEN hashtable for reference genome
01
hashmap versions
Dragmap is the Dragen mapper/aligner Open Source Software.
Assemble bacterial isolate genomes from Nanopore reads
012
contigs log raw_contigs gfa txt versions
Performs rapid genome comparisons for a group of genomes and visualize their relatedness
01
directory versions
De-replication of microbial genomes assembled from multiple samples
Export assembly segment sequences in GFA 1.0 format to FASTA format
01
fasta versions
Reads, features, variants, assemblies, alignments, genomic range trees, pangenome graphs, and a bunch of random command line tools for bioinformatics. LGPL version 3 or later.
Filter features in gzipped BED format
01
bed versions
Reads, features, variants, assemblies, alignments, genomic range trees, pangenome graphs, and a bunch of random command line tools for bioinformatics. LGPL version 3 or later.
Filter features in gzipped GFF3 format
01
gff3 versions
Reads, features, variants, assemblies, alignments, genomic range trees, pangenome graphs, and a bunch of random command line tools for bioinformatics. LGPL version 3 or later.
Split features in gzipped BED format
01
bed versions
Reads, features, variants, assemblies, alignments, genomic range trees, pangenome graphs, and a bunch of random command line tools for bioinformatics. LGPL version 3 or later.
Split features in gzipped GFF3 format
01
gff3 versions
Reads, features, variants, assemblies, alignments, genomic range trees, pangenome graphs, and a bunch of random command line tools for bioinformatics. LGPL version 3 or later.
SV callers like lumpy look at split-reads and pair distances to find structural variants. This tool is a fast way to add depth information to those calls. This can be used as additional information for filtering variants; for example we will be skeptical of deletion calls that do not have lower than average coverage compared to regions with similar gc-content.
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vcf versions
Assessment of duplication rates in RNA-Seq datasets
0101
scatter2d boxplot hist dupmatrix intercept_slope multiqc session_info versions
Dysgu calls structural variants (SVs) from mapped sequencing reads. It is designed for accurate and efficient detection of structural variations.
012012
vcf tbi versions
Perform phasing of genotyped data with or without a reference panel
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phased_variants versions
In silico prediction of E. coli serotype
01
log tsv txt versions
Fast genome-wide functional annotation through orthology assignment.
010001
annotations orthologs hits versions
Convert any PEP project or Nextflow samplesheet to any format
000
versions samplesheet_converted
Convert any PEP project or Nextflow samplesheet to any format
Provide the SNP coverage of each individual in an eigenstrat formatted dataset.
0123
tsv json versions
A set of tools to compare and manipulate the contents of EingenStrat databases, and to calculate SNP coverage statistics in such databases.
Convert a file in FASTA format to the ELFASTA format
01
elfasta log versions
elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4.
Filter, sort and markdup sam/bam files, with optional BQSR and variant calling.
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bam logs metrics recall gvcf table activity_profile assembly_regions versions
elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4.
Merge split bam/sam chunks in one file
01
bam versions
elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4.
Split bam file into manageable chunks
01
bam versions
elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4.
cons calculates a consensus sequence from a multiple sequence alignment. To obtain the consensus, the sequence weights and a scoring matrix are used to calculate a score for each amino acid residue or nucleotide at each position in the alignment.
01
consensus versions
The European Molecular Biology Open Software Suite
the revseq program from emboss reverse complements a nucleotide sequence
01
revseq versions
The European Molecular Biology Open Software Suite
EMM typing of Streptococcus pyogenes assemblies
01
tsv versions
A taxonomic profiler for metagenomic 16S data optimized for error prone long reads.
010
report assignment_report samfile unclassified_fa versions
Emu is a relative abundance estimator for 16s genomic data.
endorS.py calculates endogenous DNA from samtools flagstat files and print to screen
0123
json versions
Ensembl Variant Effect Predictor (VEP). The cache downloading options are controlled through task.ext.args.
0123
cache versions
VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
Filter variants based on Ensembl Variant Effect Predictor (VEP) annotations.
010
output versions
VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled through task.ext.args.
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vcf tbi tab json report versions
VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
Searches a term in a public NCBI database
010
xml versions
Entrez Direct (EDirect) is a method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.
Queries an NCBI database using Unique Identifier(s)
0120
xml versions
Entrez Direct (EDirect) is a method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.
Queries an NCBI database using an UID
01000
txt versions
Entrez Direct (EDirect) is a method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.
phylogenetic placement of query sequences in a reference tree
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epang jplace log versions
Massively parallel phylogenetic placement of genetic sequences
splits an alignment into reference and query parts
012
query reference versions
Massively parallel phylogenetic placement of genetic sequences
estimation of the unfolded site frequency spectrum
0123
sfs_out pvalues_out versions
Uses evigene/scripts/prot/tr2aacds.pl to filter a transcript assembly
01
dropset okayset versions
EvidentialGene is a genome informatics project for "Evidence Directed Gene Construction for Eukaryotes", for constructing high quality, accurate gene sets for animals and plants (any eukaryotes), being developed by Don Gilbert at Indiana University, gilbertd at indiana edu.
Estimate repeat sizes using NGS data
012010101
vcf json bam versions
Merge STR profiles into a multi-sample STR profile
010101
merged_profiles versions
ExpansionHunter Denovo (EHdn) is a suite of tools for detecting novel expansions of short tandem repeats (STRs).
Compute genome-wide STR profile
0120101
locus_tsv motif_tsv str_profile versions
ExpansionHunter Denovo (EHdn) is a suite of tools for detecting novel expansions of short tandem repeats (STRs).
Run falco on sequenced reads
01
html txt versions
falco is a drop-in C++ implementation of FastQC to assess the quality of sequence reads.
Aligns sequences using FAMSA
01010
alignment versions
Algorithm for large-scale multiple sequence alignments
Renders a guidetree in famsa
01
tree versions
Algorithm for large-scale multiple sequence alignments
Perform adapter and quality trimming on sequencing reads with reporting
01
reads stats debug statspdf reads_fail reads_unpaired log versions
tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.
010
log txt hmm hmm_genes orfs orfs_amino contigs contigs_pept filtered filtered_pept fragments trimmed spades metagenome tmp versions
A program that counts sequence occurrences in FASTQ files.
0101
count_matrix stats distribution_plot reads_plot reads_plot_percentage versions
2FAST2Q is ideal for CRISPRi-Seq, and for extracting and counting any kind of information from reads in the fastq format, such as barcodes in Bar-seq experiments. 2FAST2Q can work with sequence mismatches, Phred-score, and be used to find and extract unknown sequences delimited by known sequences. 2FAST2Q can extract multiple features per read using either fixed positions or delimiting search sequences.
"Python C-extension for a simple validator for fasta files. The module emits the validated file or an error log upon validation failure."
01
success_log error_log versions
"Python C-extension for a simple C code to validate a fasta file. It only checks a few things, and by default only sets its response via the return code, so you will need to check that!"
Quickly compute statistics over a fasta file in windows.
01
freq mononuc dinuc trinuc tetranuc versions
A fast K-mer counter for high-fidelity shotgun datasets
01
hist ktab prof versions
A fast K-mer counter for high-fidelity shotgun datasets
A fast K-mer counter for high-fidelity shotgun datasets
01
hist versions
A fast K-mer counter for high-fidelity shotgun datasets
A tool to merge FastK histograms
0123
hist ktab prof versions
A fast K-mer counter for high-fidelity shotgun datasets
Distance-based phylogeny with FastME
012
nwk stats matrix bootstrap versions
Perform adapter/quality trimming on sequencing reads
010000
reads json html log reads_fail reads_merged versions
fastqe is a bioinformatics command line tool that uses emojis to represent and analyze genomic data.
01
tsv versions
Build fastq screen config file from bowtie index files
00
database versions
FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.
Align reads to multiple reference genomes using fastq-screen
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txt png html fastq versions
FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.
Collapses identical sequences in a FASTQ/A file into a single sequence (while maintaining reads counts)
01
fasta versions
A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing
Run NCBI's FCS adaptor on assembled genomes
01
cleaned_assembly adaptor_report log pipeline_args skipped_trims versions
The Foreign Contamination Screening (FCS) tool rapidly detects contaminants from foreign organisms in genome assemblies to prepare your data for submission. Therefore, the submission process to NCBI is faster and fewer contaminated genomes are submitted. This reduces errors in analyses and conclusions, not just for the original data submitter but for all subsequent users of the assembly.
Run FCS-GX on assembled genomes. The contigs of the assembly are searched against a reference database excluding the given taxid.
010
fcs_gx_report taxonomy_report versions
"The Foreign Contamination Screening (FCS) tool rapidly detects contaminants from foreign organisms in genome assemblies to prepare your data for submission. Therefore, the submission process to NCBI is faster and fewer contaminated genomes are submitted. This reduces errors in analyses and conclusions, not just for the original data submitter but for all subsequent users of the assembly."
Runs FCS-GX (Foreign Contamination Screen - Genome eXtractor) to remove foreign contamination from genome assemblies
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cleaned contaminants versions
The NCBI Foreign Contamination Screen. Genomic cross-species aligner, for contamination detection.
Fetches the NCBI FCS-GX database using a provided manifest URL
0
database versions
The NCBI Foreign Contamination Screen. Genomic cross-species aligner, for contamination detection.
Runs FCS-GX (Foreign Contamination Screen - Genome eXtractor) to screen and remove foreign contamination from genome assemblies
01200
fcsgx_report taxonomy_report log hits versions
The NCBI Foreign Contamination Screen. Genomic cross-species aligner, for contamination detection.
Uses FGBIO CallDuplexConsensusReads to call duplex consensus sequences from reads generated from the same double-stranded source molecule.
0100
bam versions
A set of tools for working with genomic and high throughput sequencing data, including UMIs
Calls consensus sequences from reads with the same unique molecular tag.
0100
bam versions
Tools for working with genomic and high throughput sequencing data.
Collects a suite of metrics to QC duplex sequencing data.
010
family_sizes duplex_family_sizes duplex_yield_metrics umi_counts duplex_qc duplex_umi_counts versions
A set of tools for working with genomic and high throughput sequencing data, including UMIs
ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.
Using the fgbio tools, converts FASTQ files sequenced into unaligned BAM or CRAM files possibly moving the UMI barcode into the RX field of the reads
01
bam cram versions
A set of tools for working with genomic and high throughput sequencing data, including UMIs
Uses FGBIO FilterConsensusReads to filter consensus reads generated by CallMolecularConsensusReads or CallDuplexConsensusReads.
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bam versions
A set of tools for working with genomic and high throughput sequencing data, including UMIs
Groups reads together that appear to have come from the same original molecule. Reads are grouped by template, and then templates are sorted by the 5โ mapping positions of the reads from the template, used from earliest mapping position to latest. Reads that have the same end positions are then sub-grouped by UMI sequence. (!) Note: the MQ tag is required on reads with mapped mates (!) This can be added using samblaster with the optional argument --addMateTags.
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bam histogram versions
A set of tools for working with genomic and high throughput sequencing data, including UMIs
Sorts a SAM or BAM file. Several sort orders are available, including coordinate, queryname, random, and randomquery.
01
bam versions
Tools for working with genomic and high throughput sequencing data.
FGBIO tool to zip together an unmapped and mapped BAM to transfer metadata into the output BAM
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bam versions
A set of tools for working with genomic and high throughput sequencing data, including UMIs
Filtlong filters long reads based on quality measures or short read data.
012
reads log versions
A module for concatenation of gzipped or uncompressed files getting around UNIX terminal argument size
01
file_out versions
GNU find searches the directory tree rooted at each given starting-point by evaluating the given expression
pigz, which stands for Parallel Implementation of GZip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data.
A module for decompressing a large number of gzipped files, getting around the UNIX terminal argument limit
01
file_out versions
GNU find searches the directory tree rooted at each given starting-point by evaluating the given expression
pigz, which stands for Parallel Implementation of GZip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data.
Perform merging of mate paired-end sequencing reads
01
merged notcombined histogram versions
De novo assembler for single molecule sequencing reads
010
fasta gfa gv txt log json versions
Efficient compression tool for protein structures
01
fcz versions
Foldcomp: a library and format for compressing and indexing large protein structure sets
Decompression tool for foldcomp compressed structures
01
pdb versions
Foldcomp: a library and format for compressing and indexing large protein structure sets
Creates a database for Foldmason.
01
db versions
Multiple Protein Structure Alignment at Scale with FoldMason
Aligns protein structures using foldmason
01010
msa_3di msa_aa versions
Multiple Protein Structure Alignment at Scale with FoldMason
Renders a visualization report using foldmason
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html versions
Multiple Protein Structure Alignment at Scale with FoldMason
Create a database from protein structures
01
db versions
Foldseek: fast and accurate protein structure search
Search for protein structural hits against a foldseek database of protein structures
0101
aln versions
Foldseek: fast and accurate protein structure search
fq generate is a FASTQ file pair generator. It creates two reads, formatting names as described by Illumina. While generate creates "valid" FASTQ reads, the content of the files are completely random. The sequences do not align to any genome. This requires a seed (--seed) to be supplied in ext.args.
0
fastq versions
fq is a library to generate and validate FASTQ file pairs.
fq subsample outputs a subset of records from single or paired FASTQ files. This requires a seed (--seed) to be set in ext.args.
01
fastq versions
fq is a library to generate and validate FASTQ file pairs.
Demultiplex fastq files
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sample_fastq metrics most_frequent_unmatched versions
A haplotype-based variant detector
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vcf versions
Bootstrap sample demixing by resampling each site based on a multinomial distribution of read depth across all sites, where the event probabilities were determined by the fraction of the total sample reads found at each site, followed by a secondary resampling at each site according to a multinomial distribution (that is, binomial when there was only one SNV at a site), where event probabilities were determined by the frequencies of each base at the site, and the number of trials is given by the sequencing depth.
012000
lineages summarized versions
Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics.
specify the relative abundance of each known haplotype
01200
demix versions
Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics.
downloads new versions of the curated SARS-CoV-2 lineage file and barcodes
0
barcodes lineages_topology lineages_meta versions
Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics.
call variant and sequencing depth information of the variant
010
variants versions
Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics.
Cluster genome FASTA files by average nucleotide identity
0123
tsv dereplicated_bins versions
Gene Allele Mutation Microbial Assessment
010
gamma psl gff fasta versions
Tool for Gene Allele Mutation Microbial Assessment
Build ganon database using custom reference sequences.
01000
db info versions
ganon classifies short DNA sequences against large sets of genomic reference sequences efficiently
Classify FASTQ files against ganon database
010
tre report one all unc log versions
ganon classifies short DNA sequences against large sets of genomic reference sequences efficiently
Generate a ganon report file from the output of ganon classify
010
tre versions
ganon classifies short DNA sequences against large sets of genomic reference sequences efficiently
Generate a multi-sample report file from the output of ganon report runs
01
txt versions
ganon classifies short DNA sequences against large sets of genomic reference sequences efficiently
assigns taxonomy to query sequences in phylogenetic placement output
012
examineassign profile labelled_tree per_query krona sativa versions
Genesis Applications for Phylogenetic Placement Analysis
Grafts query sequences from phylogenetic placement on the reference tree
01
newick versions
Genesis Applications for Phylogenetic Placement Analysis
colours a phylogeny with placement densities
01
newick nexus phyloxml svg colours log versions
Genesis Applications for Phylogenetic Placement Analysis
Performs local realignment around indels to correct for mapping errors
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bam versions
The full Genome Analysis Toolkit (GATK) framework, license restricted.
Generates a list of locations that should be considered for local realignment prior genotyping.
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intervals versions
The full Genome Analysis Toolkit (GATK) framework, license restricted.
SNP and Indel variant caller on a per-locus basis
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vcf versions
The full Genome Analysis Toolkit (GATK) framework, license restricted.
Assigns all the reads in a file to a single new read-group
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bam bai cram versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Annotates intervals with GC content, mappability, and segmental-duplication content
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annotated_intervals versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Apply base quality score recalibration (BQSR) to a bam file
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bam cram versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Apply base quality score recalibration (BQSR) to a bam file
metainputinput_indexbqsr_tableintervalsfastafaidict
meta versions bam cram
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Apply a score cutoff to filter variants based on a recalibration table. AplyVQSR performs the second pass in a two-stage process called Variant Quality Score Recalibration (VQSR). Specifically, it applies filtering to the input variants based on the recalibration table produced in the first step by VariantRecalibrator and a target sensitivity value.
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vcf tbi versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Calculates the allele-specific read counts for allele-specific expression analysis of RNAseq data
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csv versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Generate recalibration table for Base Quality Score Recalibration (BQSR)
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table versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Generate recalibration table for Base Quality Score Recalibration (BQSR)
metainputinput_indexintervalsfastafaidictknown_sitesknown_sites_tbi
meta versions table
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Creates an interval list from a bed file and a reference dict
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interval_list versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Calculates the fraction of reads from cross-sample contamination based on summary tables from getpileupsummaries. Output to be used with filtermutectcalls.
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contamination segmentation versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
estimates the parameters for the DRAGstr model
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dragstr_model versions
Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Apply a Convolutional Neural Net to filter annotated variants
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vcf tbi versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Collects read counts at specified intervals. The count for each interval is calculated by counting the number of read starts that lie in the interval.
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hdf5 tsv versions
Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Gathers paired-end and split read evidence files for use in the GATK-SV pipeline. Output files are a file containing the location of and orientation of read pairs marked as discordant, and a file containing the clipping location of all soft clipped reads and the orientation of the clipping.
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split_read_evidence split_read_evidence_index paired_end_evidence paired_end_evidence_index site_depths site_depths_index versions
Genome Analysis Toolkit (GATK4)
Combine per-sample gVCF files produced by HaplotypeCaller into a multi-sample gVCF file
012000
combined_gvcf versions
Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
This tool looks for low-complexity STR sequences along the reference that are later used to estimate the Dragstr model during single sample auto calibration CalibrateDragstrModel.
000
str_table versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Merges adjacent DepthEvidence records
012000
condensed_evidence condensed_evidence_index versions
Genome Analysis Toolkit (GATK4)
Creates a panel of normals (PoN) for read-count denoising given the read counts for samples in the panel.
01
pon versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Creates a sequence dictionary for a reference sequence
01
dict versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Create a panel of normals constraining germline and artifactual sites for use with mutect2.
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vcf tbi versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Denoises read counts to produce denoised copy ratios
0101
standardized denoised versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Determines the baseline contig ploidy for germline samples given counts data
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calls model versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Estimates the numbers of unique molecules in a sequencing library.
01000
metrics versions
Genome Analysis Toolkit (GATK4)
Converts FastQ file to SAM/BAM format
01
bam versions
Genome Analysis Toolkit (GATK4) Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Filters intervals based on annotations and/or count statistics.
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interval_list versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Filters the raw output of mutect2, can optionally use outputs of calculatecontamination and learnreadorientationmodel to improve filtering.
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vcf tbi stats versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Apply tranche filtering
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vcf tbi versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Gathers scattered BQSR recalibration reports into a single file
01
table versions
Genome Analysis Toolkit (GATK4)
write your description here
010
table versions
Genome Analysis Toolkit (GATK4)
merge GVCFs from multiple samples. For use in joint genotyping or somatic panel of normal creation.
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genomicsdb updatedb intervallist versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Perform joint genotyping on one or more samples pre-called with HaplotypeCaller.
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vcf tbi versions
Genome Analysis Toolkit (GATK4)
Calls copy-number variants in germline samples given their counts and the output of DetermineGermlineContigPloidy.
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cohortcalls cohortmodel casecalls versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Summarizes counts of reads that support reference, alternate and other alleles for given sites. Results can be used with CalculateContamination. Requires a common germline variant sites file, such as from gnomAD.
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table versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Call germline SNPs and indels via local re-assembly of haplotypes
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vcf tbi bam versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Creates an index for a feature file, e.g. VCF or BED file.
01
index versions
Genome Analysis Toolkit (GATK4)
Converts an Picard IntervalList file to a BED file.
01
bed versions
Genome Analysis Toolkit (GATK4)
Splits the interval list file into unique, equally-sized interval files and place it under a directory
01
interval_list versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Uses f1r2 counts collected during mutect2 to Learn the prior probability of read orientation artifacts
01
artifactprior versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Left align and trim variants using GATK4 LeftAlignAndTrimVariants.
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vcf tbi versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.
0100
cram bam crai bai metrics versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.
metabamfastafaidict
meta versions output bam_index
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Merge unmapped with mapped BAM files
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bam versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Merges mutect2 stats generated on different intervals/regions
01
stats versions
Genome Analysis Toolkit (GATK4)
Merges several vcf files
0101
vcf tbi versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Call somatic SNVs and indels via local assembly of haplotypes.
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vcf tbi stats f1r2 versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Postprocesses the output of GermlineCNVCaller and generates VCFs and denoised copy ratios
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intervals segments denoised versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Prepares bins for coverage collection.
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interval_list versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Print reads in the SAM/BAM/CRAM file
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bam cram sam versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
WARNING - this tool is still experimental and shouldn't be used in a production setting. Gathers paired-end and split read evidence files for use in the GATK-SV pipeline. Output files are a file containing the location of and orientation of read pairs marked as discordant, and a file containing the clipping location of all soft clipped reads and the orientation of the clipping.
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printed_evidence printed_evidence_index versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Condenses homRef blocks in a single-sample GVCF
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vcf versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Reverts SAM or BAM files to a previous state.
01
bam versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Converts BAM/SAM file to FastQ format
01
fastq versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Select a subset of variants from a VCF file
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vcf tbi versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Create a fasta with the bases shifted by offset
010101
shift_fa shift_fai shift_back_chain dict intervals shift_intervals versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
EXPERIMENTAL TOOL! Convert SiteDepth to BafEvidence
01201000
baf baf_tbi versions
Genome Analysis Toolkit (GATK4)
Splits CRAM files efficiently by taking advantage of their container based structure
01
split_crams versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Split intervals into sub-interval files.
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split_intervals versions
Genome Analysis Toolkit (GATK4)
Splits reads that contain Ns in their cigar string
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bam versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Adds predicted functional consequence, gene overlap, and noncoding element overlap annotations to SV VCF from GATK-SV pipeline. Input files are an SV VCF, a GTF file containing primary or canonical transcripts, and a BED file containing noncoding elements. Output file is an annotated SV VCF.
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annotated_vcf index versions
Genome Analysis Toolkit (GATK4)
Clusters structural variants based on coordinates, event type, and supporting algorithms
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clustered_vcf clustered_vcf_index versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
This tool locates and unmark the marked duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.
01
bam bai versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Filter variants
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vcf tbi versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Build a recalibration model to score variant quality for filtering purposes. It is highly recommended to follow GATK best practices when using this module, the gaussian mixture model requires a large number of samples to be used for the tool to produce optimal results. For example, 30 samples for exome data. For more details see https://gatk.broadinstitute.org/hc/en-us/articles/4402736812443-Which-training-sets-arguments-should-I-use-for-running-VQSR-
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recal idx tranches plots versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Extract fields from a VCF file to a tab-delimited table
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table versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Apply base quality score recalibration (BQSR) to a bam file
01234000
bam cram versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Generate recalibration table for Base Quality Score Recalibration (BQSR)
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table versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.
01000
output bam_index metrics versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
If you are like many computer users, you would frequently like to make changes in various text files wherever certain patterns appear, or extract data from parts of certain lines while discarding the rest. The job is easy with awk, especially the GNU implementation gawk.
0100
output versions
GECCO is a fast and scalable method for identifying putative novel Biosynthetic Gene Clusters (BGCs) in genomic and metagenomic data using Conditional Random Fields (CRFs).
0120
genes features clusters gbk json versions
Biosynthetic Gene Cluster prediction with Conditional Random Fields.
Convert a mappability file to bedgraph format
0101
bedgraph sizes versions
GEM2 is a high-performance mapping tool. It also provide a unique tool to evaluate mappability.
Create a GEM index from a FASTA file
01
index log versions
GEM2 is a high-performance mapping tool. It also provide a unique tool to evaluate mappability.
Define the mappability of a reference
010
map versions
GEM2 is a high-performance mapping tool. It also provide a unique tool to evaluate mappability.
Create a GEM index from a FASTA file
01
index info versions
The GEM indexer (v3).
Performs fastq alignment to a fasta reference using using gem3-mapper
01010
bam versions
The GEM indexer (v3).
A derivative of GenomeScope2.0 modified to work with FastK
01
linear_plot log_plot model summary transformed_linear_plot transformed_log_plot kmer_cov versions
create index file for genmap
01
index versions
Ultra-fast computation of genome mappability.
create mappability files for a genome
0101
wig bedgraph txt csv versions
Ultra-fast computation of genome mappability.
for annotating regions, frequencies, cadd scores
01
vcf versions
Annotate genetic inheritance models in variant files
Score compounds
01
vcf versions
Annotate genetic inheritance models in variant files
annotate models of inheritance
0120
vcf versions
Annotate genetic inheritance models in variant files
Score the variants of a vcf based on their annotation
0120
vcf versions
Annotate genetic inheritance models in variant files
Download geNomad databases and related files
NO input
genomad_db versions
Identification of mobile genetic elements
Identify mobile genetic elements present in genomic assemblies
010
aggregated_classification taxonomy provirus compositions calibrated_classification plasmid_fasta plasmid_genes plasmid_proteins plasmid_summary virus_fasta virus_genes virus_proteins virus_summary versions
Identification of mobile genetic elements
Estimate genome heterozygosity, repeat content, and size from sequencing reads using a kmer-based statistical approach
01
linear_plot_png transformed_linear_plot_png log_plot_png transformed_log_plot_png model summary lookup_table fitted_histogram_png versions
Genotype Salmonella Typhi from Mykrobe results
01
tsv versions
Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
Peak-calling for ChIP-seq and ATAC-seq enrichment experiments
0120
peak versions bedgraph_pvalues bedgraph_pileup bed_intervals duplicates
geofetch is a command-line tool that downloads and organizes data and metadata from GEO and SRA
0
samples versions
Retrieves GEO data from the Gene Expression Omnibus (GEO)
01
rds expression annotation versions
Get data from NCBI Gene Expression Omnibus (GEO)
Downloads databases needed for running getorganelle
0
db versions
Get organelle genomes from genome skimming data
Assembles organelle genomes from genomic data
0101
fasta etc versions
Get organelle genomes from genome skimming data
Collapse walk-preserving shared affixes in variation graphs in GFA format
01
gfa affixes versions
A single fast and exhaustive tool for summary statistics and simultaneous fa (fasta, fastq, gfa [.gz]) genome assembly file manipulation.
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assembly_summary assembly versions
Converts GFA or rGFA files to FASTA
01
fasta versions
Tools for manipulating sequence graphs in the GFA and rGFA formats
Summary statistics for GFA files
01
stats versions
Tools for manipulating sequence graphs in the GFA and rGFA formats
Compare, merge, annotate and estimate accuracy of generated gtf files
0101201
annotated_gtf combined_gtf tmap refmap loci stats tracking versions
Validate, filter, convert and perform various other operations on GFF files
010
gtf gffread_gff gffread_fasta versions
gget is a free, open-source command-line tool and Python package that enables efficient querying of genomic databases. gget consists of a collection of separate but interoperable modules, each designed to facilitate one type of database querying in a single line of code.
01
files output versions
gget enables efficient querying of genomic databases
Defines chunks where to run imputation
0123
chunk_chr versions
GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.
Compute the r2 correlation between imputed dosages (in MAF bins) and highly-confident genotype calls from the high-coverage dataset.
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errors_cal errors_grp errors_spl rsquare_grp rsquare_spl versions
GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.
Concatenates imputation chunks in a single VCF/BCF file ligating phased information.
012
merged_variants versions
GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.
main GLIMPSE algorithm, performs phasing and imputation refining genotype likelihoods
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phased_variants versions
GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.
Generates haplotype calls by sampling haplotype estimates
01
haplo_sampled versions
GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.
Defines chunks where to run imputation
012340
chunk_chr versions
GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies.
Program to compute the genotyping error rate at the sample or marker level.
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errors_cal errors_grp errors_spl rsquare_grp rsquare_spl rsquare_per_site versions
GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies.
Ligatation of multiple phased BCF/VCF files into a single whole chromosome file. GLIMPSE2 is run in chunks that are ligated into chromosome-wide files maintaining the phasing.
012
merged_variants versions
GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies.
Tool for imputation and phasing from vcf file or directly from bam files.
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phased_variants stats_coverage versions
GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies.
Tool to create a binary reference panel for quick reading time.
0123401
bin_ref versions
GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies.
merge gVCF files and perform joint variant calling
0101
bcf versions
GMM-Demux is a Gaussian-Mixture-Model-based software for processing sample barcoding data (cell hashing and MULTI-seq).
0120000
barcodes matrix features classification_report config_report summary_report versions
Writes a sorted concatenation of file/s
01
sorted versions
Writes a sorted concatenation of file/s
Split a file into consecutive or interleaved sections
01
split versions
The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system.
Query metadata for any taxon across the tree of life.
012
taxonsearch versions
goat-cli is a command line interface to query the Genomes on a Tree Open API.
Quickly estimate coverage from a whole-genome bam or cram index. A bam index has 16KB resolution so that's what this gives, but it provides what appears to be a high-quality coverage estimate in seconds per genome.
01201
output ped bed bed_index roc html png versions
goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary
runs a functional enrichment analysis with gprofiler2
010101
all_enrich rds plot_png plot_html sub_enrich sub_plot filtered_gmt session_info versions
An R interface corresponding to the 2019 update of g:Profiler web tool.
Checks if the input file is bgzip compressed or not
01
compress_bgzip versions
a wee tool for random access into BGZF files.
A versatile pairwise aligner for genomic and spliced nucleotide sequences
0
index versions
A versatile pairwise aligner for genomic and spliced nucleotide sequences.
Tools for population-scale genotyping using pangenome graphs.
01
vcf tbi versions
A graph-based variant caller capable of genotyping population-scale short read data sets while incorporating previously discovered variants.
GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.
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bedpe bed versions
GRIDSS: the Genomic Rearrangement IDentification Software Suite
GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.
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vcf versions
GRIDSS: the Genomic Rearrangement IDentification Software Suite
GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.
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bedpe bed versions
GRIDSS: the Genomic Rearrangement IDentification Software Suite
GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.
0101
high_conf_sv all_sv versions
GRIDSS: the Genomic Rearrangement IDentification Software Suite
GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.
0101
high_conf_sv all_sv versions
GRIDSS: the Genomic Rearrangement IDentification Software Suite
run the Broad Gene Set Enrichment tool in GSEA mode
01230101
rpt index_html heat_map_corr_plot report_tsvs_ref report_htmls_ref report_tsvs_target report_htmls_target ranked_gene_list gene_set_sizes histogram heatmap pvalues_vs_nes_plot ranked_list_corr butterfly_plot gene_set_tsv gene_set_html gene_set_heatmap snapshot gene_set_enplot gene_set_dist archive versions
Gene Set Enrichment Analysis (GSEA)
Collapse redundant transcript models in Iso-Seq data.
010
bed bed_trans_reads local_density_error polya read strand_check trans_report versions varcov variants
Collapse similar gene model
Merge multiple transcriptomes while maintaining source information.
010
bed gene_report merge trans_report versions
Gene-Switch Transcriptome Annotation by Modular Algorithms
Helper script, remove remaining polyA sequences from Full Length Non Chimeric reads (Pacbio isoseq3)
01
fasta report tails versions
Gene-Switch Transcriptome Annotation by Modular Algorithms
GenomeTools gt-gff3 utility to parse, possibly transform, and output GFF3 files
01
gt_gff3 error_log versions
The GenomeTools genome analysis system
GenomeTools gt-gff3validator utility to strictly validate a GFF3 file
01
success_log error_log versions
The GenomeTools genome analysis system
Predicts LTR retrotransposons using GenomeTools gt-ltrharvest utility
01
tabout gff3 fasta inner_fasta versions
The GenomeTools genome analysis system
GenomeTools gt-stat utility to show statistics about features contained in GFF3 files
01
stats versions
The GenomeTools genome analysis system
Computes enhanced suffix array using GenomeTools gt-suffixerator utility
010
index versions
The GenomeTools genome analysis system
GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB.
010100
summary tree markers msa user_msa filtered failed log warnings versions
GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB.
Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions.
0
fasta gff vcf stats phylip embl_predicted embl_branch tree tree_labelled versions
Download database for GUNC detection of Chimerism and Contamination in Prokaryotic Genomes
0
db versions
Python package for detection of chimerism and contamination in prokaryotic genomes.
Merging of CheckM and GUNC results in one summary table
012
tsv versions
Python package for detection of chimerism and contamination in prokaryotic genomes.
Detection of Chimerism and Contamination in Prokaryotic Genomes
010
maxcss_level_tsv all_levels_tsv versions
Python package for detection of chimerism and contamination in prokaryotic genomes.
Removes all non-variant blocks from a gVCF file to produce a smaller variant-only VCF file.
01
vcf versions
gvcftools is a package of small utilities for creating and analyzing gVCF files
Tool to convert and summarize ABRicate outputs using the hAMRonization specification
01000
json tsv versions
Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification
Tool to convert and summarize AMRfinderPlus outputs using the hAMRonization specification.
01000
json tsv versions
Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification
Tool to convert and summarize DeepARG outputs using the hAMRonization specification
01000
json tsv versions
Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification
Tool to convert and summarize fARGene outputs using the hAMRonization specification
01000
json tsv versions
Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification
Tool to convert and summarize RGI outputs using the hAMRonization specification.
01000
json tsv versions
Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification
Tool to summarize and combine all hAMRonization reports into a single file
00
json tsv html versions
Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification
Haplocheck detects contamination patterns in mtDNA AND WGS sequencing studies by analyzing the mitochondrial DNA. Haplocheck also works as a proxy tool for nDNA studies and provides users a graphical report to investigate the contamination further. Internally, it uses the Haplogrep tool, that supports rCRS and RSRS mitochondrial versions.
01
txt html versions
classification into haplogroups
010
txt versions
A tool for mtDNA haplogroup classification.
classification into haplogroups
01
txt versions
A tool for mtDNA haplogroup classification.
Somatic VCF Feature Extraction tool from hap.y.
012340101
features versions
Haplotype VCF comparison tools
Hap.py is a tool to compare diploid genotypes at haplotype level. Rather than comparing VCF records row by row, hap.py will generate and match alternate sequences in a superlocus. A superlocus is a small region of the genome (sized between 1 and around 1000 bp) that contains one or more variants.
012340101010101
summary_csv roc_all_csv roc_indel_locations_csv roc_indel_locations_pass_csv roc_snp_locations_csv roc_snp_locations_pass_csv extended_csv runinfo metrics_json vcf tbi versions
Haplotype VCF comparison tools
Pre.py is a preprocessing tool made to preprocess VCF files for Hap.py
0120101
preprocessed_vcf versions
Haplotype VCF comparison tools
Hap.py is a tool to compare diploid genotypes at haplotype level. som.py is a part of hap.py compares somatic variations.
012340101010101
features metrics stats versions
Haplotype VCF comparison tools somatic variant comparison
HelitronScanner scanHead and scanTail tools for Helitron transposons in genomes
01000
scan versions
HelitronScanner uncovers a large overlooked cache of Helitron transposons in many genomes
Reformat a Multiple Sequence Alignment (MSA) file
0100
msa versions
HH-suite3 for fast remote homology detection and deep protein annotation
Identify cap locus serotype and structure in your Haemophilus influenzae assemblies
0100
gbk svg tsv versions
Computes PCA eigenvectors for a Hi-C matrix.
01
results pca1 pca2 versions
Set of programs to process, analyze and visualize Hi-C and capture Hi-C data
Whole-genome assembly using PacBio HiFi reads
01201201201
raw_unitigs bin_files processed_unitigs primary_contigs alternate_contigs hap1_contigs hap2_contigs corrected_reads read_overlaps log versions
Align RNA-Seq reads to a reference with HISAT2
010101
bam summary fastq versions
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome.
Builds HISAT2 index for reference genome
010101
index versions
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome.
Extracts splicing sites from a gtf files
01
txt versions
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome.
Pre-compute the graph index structure.
01
graph versions
HLA typing from short and long reads
Performs HLA typing based on a population reference graph and employs a new linear projection method to align reads to the graph.
0123
results extraction extraction_mapped extraction_unmpapped hla fastq reads_per_level remapped versions
HLA typing from short and long reads
gcCounter function from HMMcopy utilities, used to generate GC content in non-overlapping windows from a fasta reference
01
wig versions
C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy
Perl script (generateMap.pl) generates the mappability of a genome given a certain size of reads, for input to hmmcopy mapcounter. Takes a very long time on large genomes, is not parallelised at all.
01
bigwig versions
C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy
mapCounter function from HMMcopy utilities, used to generate mappability in non-overlapping windows from a bigwig file
01
wig versions
C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy
readCounter function from HMMcopy utilities, used to generate read in windows
012
wig versions
C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy
Mask multiple sequence alignments
012345670
maskedaln fmask_rf fmask_all gmask_rf gmask_all pmask_rf pmask_all versions
Biosequence analysis using profile hidden Markov models
reformats sequence files, see HMMER documentation for details. The module requires that the format is specified in ext.args in a config file, and that this comes last. See the tools help for possible values.
01
seqreformated versions
Biosequence analysis using profile hidden Markov models
hmmalign from the HMMER suite aligns a number of sequences to an HMM profile
010
sto versions
Biosequence analysis using profile hidden Markov models
create an hmm profile from a multiple sequence alignment
010
hmm hmmbuildout versions
Biosequence analysis using profile hidden Markov models
extract hmm from hmm database file or create index for hmm database
01000
hmm index versions
Biosequence analysis using profile hidden Markov models
compress and index profile database for hmmscan
01
compressed_db versions
Biosequence analysis using profile hidden Markov models
R script that scores output from multiple runs of hmmer/hmmsearch
01
hmmrank versions
Biosequence analysis using profile hidden Markov models
A Language and Environment for Statistical Computing
Tidyverse: R packages for data science
search profile(s) against a sequence database
012345
output alignments target_summary domain_summary versions
Biosequence analysis using profile hidden Markov models
Human mitochondrial variants annotation using HmtVar. Contains .plk file with annotation, so can be run offline
01
vcf versions
Human mitochondrial variants annotation using HmtVar.
Annotate peaks with HOMER suite
0100
txt stats versions
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.
Find peaks with HOMER suite
010
txt versions
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.
Create a tag directory with the HOMER suite
010
tagdir taginfo versions
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
Differential gene expression analysis based on the negative binomial distribution
Empirical Analysis of Digital Gene Expression Data in R
Create a UCSC bed graph with the HOMER suite
01
bedGraph versions
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.
Converting from HOMER peak to BED file formats
01
bed versions
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.
write your description here
0100
fastq json versions
Hostile: accurate host decontamination
Downloads required reference genomes for Hostile
NO input
reference versions
Hostile: accurate host decontamination
Serotype prediction of Haemophilus parasuis assemblies
01
tsv versions
count how many reads map to each feature
01201
txt versions
HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
This tools takes a background VCF, such as gnomad, that has full genome (though in some cases, users will instead want whole exome) coverage and uses that as an expectation of variants.
012012
tsv versions
useful command-line tools written to show-case hts-nim
HUMID is a tool to quickly and easily remove duplicate reads from FastQ files, with or without UMIs.
0101
log dedup annotated stats versions
ichorCNA is an R package for calculating copy number alteration from (low-pass) whole genome sequencing, particularly for use in cell-free DNA. This module generates a panel of normals
000000
rds txt versions
Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
ichorCNA is an R package for calculating copy number alteration from (low-pass) whole genome sequencing, particularly for use in cell-free DNA
010000000
rdata seg cna_seg seg_txt corrected_depth ichorcna_params plots genome_plot versions
Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
Plot a metagene of cross-link events/sites around various transcriptomic landmarks.
010
tsv versions
Computational pipeline for analysis of iCLIP data
Runs iCount peaks on a BED file of crosslinks
012
peaks versions
Computational pipeline for analysis of iCLIP data
Formats a GTF file for use with iCount sigxls
010
gtf regions versions
Computational pipeline for analysis of iCLIP data
Runs iCount sigxls on a BED file of crosslinks
010
sigxls scores versions
Computational pipeline for analysis of iCLIP data
Report proportion of cross-link events/sites on each region type.
010
summary_type summary_subtype summary_gene versions
Computational pipeline for analysis of iCLIP data
Demultiplex paired-end FASTQ files from QuantSeq-Pool
012
fastq undetermined stats versions
igv.js is an embeddable interactive genome visualization component
012
browser align_files index_files versions
Create an embeddable interactive genome browser component. Output files are expected to be present in the same directory as the genome browser html file. To visualise it, files have to be served. Check the documentation at: https://github.com/igvteam/igv-webapp for an example and https://github.com/igvteam/igv.js/wiki/Data-Server-Requirements for server requirements
A Python application to generate self-contained HTML reports for variant review and other genomic applications
0123012
report versions
Ilastik is a tool that utilizes machine learning algorithms to classify pixels, segment, track and count cells in images. Ilastik contains a graphical user interface to interactively label pixels. However, this nextflow module will implement the --headless mode, to apply pixel classification using a pre-trained .ilp file on an input image.
0120
mask versions
Ilastik is a user friendly tool that enables pixel classification, segmentation and analysis.
Ilastik is a tool that utilizes machine learning algorithms to classify pixels, segment, track and count cells in images. Ilastik contains a graphical user interface to interactively label pixels. However, this nextflow module will implement the --headless mode, to apply pixel classification using a pre-trained .ilp file on an input image.
01230
output versions
Ilastik is a user friendly tool that enables pixel classification, segmentation and analysis.
Perform immune cell deconvolution using RNA-seq data and various computational methods.
01230
deconv_table deconv_plots versions
Search covariance models against a sequence database
01200
output alignments target_summary versions
Infernal is for searching DNA sequence databases for RNA structure and sequence similarities.
inStrain is python program for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification
01000
profile snvs gene_info genome_info linkage mapping_info scaffold_info versions
Calculation of strain-level metrics
Detect integrons in DNA sequences
01
gbk integrons summary out versions
Produces protein annotations and predictions from an amino acids FASTA file
010
tsv xml gff3 json versions
Download, extract, and check md5 of iPHoP databases
NO input
iphop_db versions
Predict host genus from genomes of uncultivated phages.
Predict phage host using iPHoP
010
iphop_genus iphop_genome iphop_detailed_output versions
Predict host genus from genomes of uncultivated phages.
Produces a Newick format phylogeny from a multiple sequence alignment using the maximum likelihood algorithm. Capable of bacterial genome size alignments.
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phylogeny report mldist lmap_svg lmap_eps lmap_quartetlh sitefreq_out bootstrap state contree nex splits suptree alninfo partlh siteprob sitelh treels rate mlrate exch_matrix log versions
Quantification of transposable elements expression in scRNA-seq
0100
versions results counts log tmp
Genomic island prediction in bacterial and archaeal genomes
01
gff log versions
IsoSeq - Cluster - Cluster trimmed consensus sequences
01
bam pbi cluster cluster_report transcriptset hq_bam hq_pbi lq_bam lq_pbi singletons_bam singletons_pbi versions
IsoSeq - Cluster - Cluster trimmed consensus sequences
Remove polyA tail and artificial concatemers
010
bam pbi consensusreadset summary report versions
IsoSeq - Scalable De Novo Isoform Discovery
IsoSeq3 - Cluster - Cluster trimmed consensus sequences
metabam
meta version bam pbi cluster cluster_report transcriptset hq_bam hq_pbi lq_bam lq_pbi singletons_bam singletons_pbi
IsoSeq3 - Cluster - Cluster trimmed consensus sequences
Remove polyA tail and artificial concatemers
metabamprimers
meta bam pbi consensusreadset summary report versions
IsoSeq3 - Scalable De Novo Isoform Discovery
Extract UMI and cell barcodes
010
bam pbi versions
Iso-Seq - Scalable De Novo Isoform Discovery
Generate a consensus sequence from a BAM file using iVar
0100
fasta qual mpileup versions
iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.
Trim primer sequences rom a BAM file with iVar
0120
bam log versions
iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.
Call variants from a BAM file using iVar
010000
tsv mpileup versions
iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.
Render jupyter (or jupytext) notebooks to HTML reports. Supports parametrization through papermill.
0100
report artifacts versions
Jupyter notebooks as plain text scripts or markdown documents
Parameterize, execute, and analyze notebooks
Parameterize, execute, and analyze notebooks
Extract BED file from hts files containing a dictionary (VCF,BAM, CRAM, DICT, etc...)
01
bed versions
Java utilities for Bioinformatics.
Convert sam files to tsv files
01230123
tsv versions
Java utilities for Bioinformatics.
Convert VCF to a user friendly table
012301
output versions
Java utilities for Bioinformatics.
View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
Filtering VCF with dynamically-compiled java expressions
01230101010101
vcf tbi csi versions
Java utilities for Bioinformatics.
View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
annotate VCF files for poly repeats
01010101
vcf tbi csi versions
Java utilities for Bioinformatics.
View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
Plot whole genome coverage from BAM/CRAM file as SVG
012010101
output versions
Java utilities for Bioinformatics.
Taxonomic classification of metagenomic sequence data using a protein reference database
010
results versions
Fast and sensitive taxonomic classification for metagenomics
Convert Kaiju's tab-separated output file into a tab-separated text file which can be imported into Krona.
010
txt versions
Fast and sensitive taxonomic classification for metagenomics
write your description here
0100
summary versions
Fast and sensitive taxonomic classification for metagenomics
Merge two tab-separated output files of Kaiju and Kraken in the column format
0120
merged versions
Fast and sensitive taxonomic classification for metagenomics
Make Kaiju FMI-index file from a protein FASTA file
010
fmi bwt sa versions
Fast and sensitive taxonomic classification for metagenomics
Aligns sequences using kalign
010
alignment versions
Kalign is a fast and accurate multiple sequence alignment algorithm.
Create kallisto index
01
index versions
Quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
Computes equivalence classes for reads and quantifies abundances
01010000
results json_info log versions
Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
quantifies scRNA-seq data from fastq files using kb-python.
01000000
count versions matrix
kallisto and bustools are wrapped in an easy-to-use program called kb
index creation for kb count quantification of single-cell data.
000
versions index t2g cdna intron cdna_t2c intron_t2c
kallisto|bustools (kb) is a tool developed for fast and efficient processing of single-cell OMICS data.
Module that calls normalize-by-median.py from khmer. The module can take a mix of paired end (interleaved) and single end reads. If both types are provided, only a single file with single ends is possible.
000
reads versions
khmer k-mer counting library
Removes low abundance k-mers from FASTA/FASTQ files
01
trimmed versions
khmer k-mer counting library
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
00
report kmers versions
khmer k-mer counting library
Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC).
01
txt versions
Generate k-mers (sketches) from FASTA/Q sequences
01
outdir info versions
Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping
Construct KMCP database from k-mer files
01
kmcp log versions
Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping
Merge search results from multiple databases.
01
result versions
Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping
Generate taxonomic profile from search results
010
profile versions
Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping
Search sequences against database
010
result versions
Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping
Adds fasta files to a Kraken2 taxonomic database
010000
db versions
Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.
Builds Kraken2 database
010
db versions
Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.
Downloads and builds Kraken2 standard database
0
db versions
Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.
Classifies metagenomic sequence data
01000
classified_reads_fastq unclassified_reads_fastq classified_reads_assignment report versions
Kraken2 is a taxonomic sequence classifier that assigns taxonomic labels to sequence reads
Takes multiple kraken-style reports and combines them into a single report file
01
txt versions
KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs.
Extract reads classified at any user-specified taxonomy IDs.
0010101
extracted_kraken2_reads versions
KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs.
Takes a Kraken report file and prints out a krona-compatible TEXT file
01
txt versions
KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs.
Download and build (custom) KrakenUniq databases
01230
db versions
Metagenomics classifier with unique k-mer counting for more specific results
Download KrakenUniq databases and related fles
0
output versions
Metagenomics classifier with unique k-mer counting for more specific results
Classifies metagenomic sequence data using unique k-mer counts
012000000
classified_reads unclassified_reads classified_assignment report versions
Metagenomics classifier with unique k-mer counting for more specific results
KronaTools Update Taxonomy downloads a taxonomy database
NO input
db versions
Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
KronaTools Import Taxonomy imports taxonomy classifications and produces an interactive Krona plot.
010
html versions
Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
Creates a Krona chart from text files listing quantities and lineages.
01
html versions
Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
KronaTools Update Taxonomy downloads a taxonomy database
NO input
db versions
Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
Aligns query sequences to target sequences indexed with lastdb
0120
maf multiqc versions
LAST finds & aligns related regions of sequences.
Prepare sequences for subsequent alignment with lastal.
01
index versions
LAST finds & aligns related regions of sequences.
Converts MAF alignments in another format.
012010101
axt_gz bam blast_gz blasttab_gz chain_gz cram gff_gz html_gz psl_gz sam_gz tab_gz versions
LAST finds & aligns related regions of sequences.
Reorder alignments in a MAF file
01
maf versions
LAST finds & aligns related regions of sequences.
Post-alignment masking
01
maf versions
LAST finds & aligns related regions of sequences.
Find suitable score parameters for sequence alignment
010
param_file multiqc versions
LAST finds & aligns related regions of sequences.
Align sequences using learnMSA
01
alignment versions
learnMSA: Learning and Aligning large Protein Families
Bayesian reconstruction of ancient DNA fragments
01
bam fq_pass fq_fail unmerged_r1_fq_pass unmerged_r1_fq_fail unmerged_r2_fq_pass unmerged_r2_fq_fail log versions
Typing of clinical and environmental isolates of Legionella pneumophila
01
tsv versions
Index chain files for lift over
010
clft versions
Fast and accurate coordinate conversion between assemblies
Converting aligned short and long reads records from one reference to another
0101
bam versions
Fast and accurate coordinate conversion between assemblies
runs a differential expression analysis with Limma
0123012
results md_plot rdata model session_info normalised_counts versions
Linear Models for Microarray Data
Serogrouping Listeria monocytogenes assemblies
01
tsv versions
Lofreq subcommand to for insert base and indel alignment qualities
010
bam versions
A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data
Lofreq subcommand to call low frequency variants from alignments
0120
vcf versions
A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data
It predicts variants using multiple processors
01230101
vcf tbi versions
Lofreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It's call-parallel programme predicts variants using multiple processors
Lofreq subcommand to remove variants with low coverage or strand bias potential
01
vcf versions
A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data
Inserts indel qualities in a BAM file
0101
bam versions
Lofreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It's indelqual programme inserts indel qualities in a BAM file
Lofreq subcommand to call low frequency variants from alignments when tumor-normal paired samples are available
0123450101
vcf versions
A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data
Lofreq subcommand to call low frequency variants from alignments when tumor-normal paired samples are available
0101
bam versions
A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data
LongPhase is an ultra-fast program for simultaneously co-phasing SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms.
0123450101
bam log versions
LongPhase is an ultra-fast program for simultaneously co-phasing SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms.
LongPhase is an ultra-fast program for simultaneously co-phasing SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms.
0123450101
vcf versions
LongPhase is an ultra-fast program for simultaneously co-phasing SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms.
Finds full-length LTR retrotranspsons in genome sequences using the parallel version of LTR_Finder
01
scn gff versions
A Perl wrapper for LTR_FINDER
An efficient program for finding full-length LTR retrotranspsons in genome sequences
Predicts LTR retrotransposons using the parallel version of GenomeTools gt-ltrharvest utility included in the EDTA toolchain
01
gff3 scn versions
A Perl wrapper for LTR_harvest
The GenomeTools genome analysis system
Identifies LTR retrotransposons using LTR_retriever
metagenomeharvestfindermgescannon_tgca
meta log pass_list pass_list_gff ltrlib annotation_out annotation_gff versions
Sensitive and accurate identification of LTR retrotransposons
Estimates the mean LTR sequence identity in the genome. The input genome fasta should have short alphanumeric IDs without comments
01000
log lai_out versions
Assessing genome assembly quality using the LTR Assembly Index (LAI)
Identifies LTR retrotransposons using LTR_retriever
010000
log pass_list pass_list_gff ltrlib annotation_out annotation_gff versions
Sensitive and accurate identification of LTR retrotransposons
A tool that mines antimicrobial peptides (AMPs) from (meta)genomes by predicting peptides from genomes (provided as contigs) and outputs all the predicted anti-microbial peptides found.
01
smorfs all_orfs amp_prediction readme_file log_file versions
A pipeline for AMP (antimicrobial peptide) prediction
Peak calling of enriched genomic regions of ChIP-seq and ATAC-seq experiments
0120
peak xls versions gapped bed bdg
Model Based Analysis for ChIP-Seq data
Peak calling of enriched genomic regions of ChIP-seq and ATAC-seq experiments
0120
peak xls versions gapped bed bdg
Model Based Analysis for ChIP-Seq data
Multiple sequence alignment using MAFFT
0101010101010
fas versions
Parallel implementation of the gzip algorithm.
Multiple sequence alignment using MAFFT
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fas versions
Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform
Parallel implementation of the gzip algorithm.
Guide tree rendering using MAFFT
01
tree versions
Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform
mageck count for functional genomics, reads are usually mapped to a specific sgRNA
010
count norm versions
MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), an algorithm to process, QC, analyze and visualize CRISPR screening data.
maximum-likelihood analysis of gene essentialities computation
010
gene_summary sgrna_summary versions
MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), an algorithm to process, QC, analyze and visualize CRISPR screening data.
Mageck test performs a robust ranking aggregation (RRA) to identify positively or negatively selected genes in functional genomics screens.
01
gene_summary sgrna_summary r_script versions
MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), an algorithm to process, QC, analyze and visualize CRISPR screening data.
Multiple Sequence Alignment using Graph Clustering
01010
alignment versions
Multiple Sequence Alignment using Graph Clustering
Multiple Sequence Alignment using Graph Clustering
01
tree versions
Multiple Sequence Alignment using Graph Clustering
MALT, an acronym for MEGAN alignment tool, is a sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics.
0000
index versions log
A tool for mapping metagenomic data
MALT, an acronym for MEGAN alignment tool, is a sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics.
010
rma6 alignments log versions
A tool for mapping metagenomic data
Tool for evaluation of MALT results for true positives of ancient metagenomic taxonomic screening
0100
results versions
Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. This script reformats inversions into single inverted sequence junctions which was the format used in Manta versions <= 1.4.0.
0101
vcf tbi versions
Structural variant and indel caller for mapped sequencing data
Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs.
0123401010
candidate_small_indels_vcf candidate_small_indels_vcf_tbi candidate_sv_vcf candidate_sv_vcf_tbi diploid_sv_vcf diploid_sv_vcf_tbi versions
Structural variant and indel caller for mapped sequencing data
Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs.
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candidate_small_indels_vcf candidate_small_indels_vcf_tbi candidate_sv_vcf candidate_sv_vcf_tbi diploid_sv_vcf diploid_sv_vcf_tbi somatic_sv_vcf somatic_sv_vcf_tbi versions
Structural variant and indel caller for mapped sequencing data
Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs.
0123401010
candidate_small_indels_vcf candidate_small_indels_vcf_tbi candidate_sv_vcf candidate_sv_vcf_tbi tumor_sv_vcf tumor_sv_vcf_tbi versions
Structural variant and indel caller for mapped sequencing data
Create mapAD index for reference genome
01
index versions
An aDNA aware short-read mapper
Map short-reads to an indexed reference genome
01010000000
bam versions
An aDNA aware short-read mapper
Computational framework for tracking and quantifying DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.
010
runtime_log fragmisincorporation_plot length_plot misincorporation lgdistribution dnacomp stats_out_mcmc_hist stats_out_mcmc_iter stats_out_mcmc_trace stats_out_mcmc_iter_summ_stat stats_out_mcmc_post_pred stats_out_mcmc_correct_prob dnacomp_genome rescaled pctot_freq pgtoa_freq fasta folder versions
Screens query sequences against large sequence databases
0101
screen versions
Fast sequence distance estimator that uses MinHash
Creates vastly reduced representations of sequences using MinHash
01
mash stats versions
Fast sequence distance estimator that uses MinHash
MaxBin is a software that is capable of clustering metagenomic contigs
0123
binned_fastas summary abundance log marker_counts unbinned_fasta tooshort_fasta marker_bins marker_genes versions
Run standard proteomics data analysis with MaxQuant, mostly dedicated to label-free. Paths to fasta and raw files needs to be marked by "PLACEHOLDER"
0120
maxquant_txt versions
MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. License restricted.
Mcquant extracts single-cell data given a multi-channel image and a segmentation mask.
010101
csv versions
Analysis of mcr-1 gene (mobilized colistin resistance) for sequence variation
01
tsv fa versions
Staging module for MCMICRO transforming Imaging Mass Cytometry .txt files to .tif files with OME-XML metadata. Includes optional hot pixel removal.
01
tif versions
Staging modules for MCMICRO
Staging module for MCMICRO transforming PhenoImager .tif files into stacked and normalized ome-tif files per cycle, compatible as ASHLAR input.
01
tif versions
Staging modules for MCMICRO
mdust from DFCI Gene Indices Software Tools for masking low-complexity DNA sequences
01
fasta versions
Analyses a DAA file and exports information in text format
010
txt_gz megan versions
A tool for studying the taxonomic content of a set of DNA reads
Analyses an RMA file and exports information in text format
010
txt megan_summary versions
A tool for studying the taxonomic content of a set of DNA reads
Performs taxonomic profiling of long metagenomic reads against the melon database
0100
tsv_output json_output log versions
Serotyping of Neisseria meningitidis assemblies
01
tsv versions
Compare k-mer frequency in reads and assembly to devise the metrics K and QV
0101000
hist log_stderr versions
Merfin (k-mer based finishing tool) is a suite of subtools to variant filtering, assembly evaluation and polishing via k-mer validation. The subtool -hist estimates the QV (quality value of Merqury) for each scaffold/contig and genome-wide averages. In addition, Merfin produces a QV* estimate, which accounts also for kmers that are seen in excess with respect to their expected multiplicity predicted from the reads.
k-mer based assembly evaluation.
metameryl_dbassembly
meta versions assembly_only_kmers_bed assembly_only_kmers_wig stats dist_hist spectra_cn_fl_png spectra_cn_ln_png spectra_cn_st_png spectra_cn_hist spectra_asm_fl_png spectra_asm_ln_png spectra_asm_st_png spectra_asm_hist assembly_qv scaffold_qv read_ploidy
A script to generate hap-mer dbs for trios
0100
mat_hapmer_meryl pat_hapmer_meryl inherited_hapmers_fl_png inherited_hapmers_ln_png inherited_hapmers_st_png versions
Evaluate genome assemblies with k-mers and more.
k-mer based assembly evaluation.
012
assembly_only_kmers_bed assembly_only_kmers_wig stats dist_hist spectra_cn_fl_png spectra_cn_hist spectra_cn_ln_png spectra_cn_st_png spectra_asm_fl_png spectra_asm_hist spectra_asm_ln_png spectra_asm_st_png assembly_qv scaffold_qv read_ploidy hapmers_blob_png versions
Evaluate genome assemblies with k-mers and more.
Produces maternal and paternal FastK kmer tables from maternal, paternal and child FastK tables
010101
mat_hap_ktab pat_hap_ktab versions
FastK based version of Merqury
A reimplemenation of Kat Comp to work with FastK databases
01234
filled line stacked versions
FastK based version of Merqury
A reimplemenation of KatGC to work with FastK databases
012
filled_gc_plot line_gc_plot stacked_gc_plot versions
FastK based version of Merqury
FastK based version of Merqury
012340101
stats bed assembly_qv spectra_cn_fl spectra_cn_ln spectra_cn_st qv spectra_asm_fl spectra_asm_ln spectra_asm_st phased_block_bed phased_block_stats continuity_N block_N block_blob hapmers_blob versions
FastK based version of Merqury
An improved version of Smudgeplot using FastK
012
filled_ploidy_plot line_ploidy_plot stacked_ploidy_plot versions
FastK based version of Merqury
A genomic k-mer counter (and sequence utility) with nice features.
010
meryl_db versions
A genomic k-mer counter (and sequence utility) with nice features.
A genomic k-mer counter (and sequence utility) with nice features.
010
hist versions
A genomic k-mer counter (and sequence utility) with nice features.
A genomic k-mer counter (and sequence utility) with nice features.
010
meryl_db versions
A genomic k-mer counter (and sequence utility) with nice features.
Depth computation per contig step of metabat2
012
depth versions
Metagenome binning
Metagenome binning of contigs
012
tooshort lowdepth unbinned membership fasta versions
Metagenome binning
Annotation of eukaryotic metagenomes using MetaEuk
010
faa codon tsv gff versions
MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics
Strain-level metagenomic assignment
012340
wimp evidence_unknown_species reads2taxon em contig_coverage length_and_id krona versions
MetaMaps is a tool for long-read metagenomic analysis
Maps long reads to a metamaps database
010
classification_res meta_file meta_unmappedreadsLengths para_file versions
MetaMaps is a tool for long-read metagenomic analysis
Metagenome assembler for long-read sequences (HiFi and ONT).
010
contigs log versions
MetaMDBG: a lightweight assembler for long and accurate metagenomics reads.
Build MetaPhlAn database for taxonomic profiling.
NO input
db versions
Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance
Merges output abundance tables from MetaPhlAn4
01
txt versions
Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance
MetaPhlAn is a tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
010
profile biom bt2out versions
Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance
Merges output abundance tables from MetaPhlAn3
01
txt versions
Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance
MetaPhlAn is a tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
010
profile biom bt2out versions
Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance
Extracts per-base methylation metrics from alignments
01200
bedgraph methylkit versions
Methylation caller from MethylDackel, a (mostly) universal methylation extractor for methyl-seq experiments.
Generates methylation bias plots from alignments
01200
txt versions
Read position methylation bias tools from MethylDackel, a (mostly) universal extractor for methyl-seq experiments.
Demultiplex MGI fastq files
012
fastq undetermined ambiguous undetermined_reports ambiguous_reports general_info_reports index_reports sample_stat_reports qc_reports versions
Demultiplex MGI fastq files
A tool to estimate bacterial species abundance
0100
results versions
An integrated pipeline for estimating strain-level genomic variation from metagenomic data
marks duplicate spots along gridline edges.
01
marked_dups_spots versions
Takes a single panorama image and fills the empty grid lines with neighbour-weighted values.
Takes a single panorama image and fills the empty grid lines with neighbour-weighted values.
01
tiff versions
Mindagap is a collection of tools to process multiplexed FISH data, such as produced by Resolve Biosciences Molecular Cartography.
Minia is a short-read assembler based on a de Bruijn graph
01
contigs unitigs h5 versions
Compression of a reference panel for genotype imputation to .msav format
012
msav versions
Computationally efficient genotype imputation
Imputation of genotypes using a reference panel
0123456
vcf versions
Computationally efficient genotype imputation
Provides fasta index required by minimap2 alignment.
01
index versions
A versatile pairwise aligner for genomic and spliced nucleotide sequences.
Provides fasta index required by miniprot alignment.
01
index versions
A versatile pairwise aligner for genomic and protein sequences.
miRanda is an algorithm for finding genomic targets for microRNAs
010
txt versions
miRDeep2 Mapper is a tool that prepares deep sequencing reads for downstream miRNA detection by collapsing reads, mapping them to a genome, and outputting the required files for miRNA discovery.
0101
outputs versions
miRDeep2 Mapper (mapper.pl) is part of the miRDeep2 suite. It collapses identical reads, maps them to a reference genome, and outputs both collapsed FASTA and ARF files for downstream miRNA detection and analysis.
miRDeep2 is a tool for identifying known and novel miRNAs in deep sequencing data by analyzing sequenced RNAs. It integrates the mapping of sequencing reads to the genome and predicts miRNA precursors and mature miRNAs.
012010123
outputs versions
miRDeep2 is a tool that discovers microRNA genes by analyzing sequenced RNAs.
It includes three main scripts: miRDeep2.pl, mapper.pl, and quantifier.pl for comprehensive miRNA detection and quantification.
mirtop counts generates a file with the minimal information about each sequence and the count data in columns for each samples.
0101012
tsv versions
Small RNA-seq annotation
mirtop export generates files such as fasta, vcf or compatible with isomiRs bioconductor package
0101012
tsv fasta vcf versions
Small RNA-seq annotation
mirtop gff generates the GFF3 adapter format to capture miRNA variations
0101012
gff versions
Small RNA-seq annotation
mirtop gff gets the number of isomiRs and miRNAs annotated in the GFF file by isomiR category.
01
txt log versions
Small RNA-seq annotation
A tool for quality control and tracing taxonomic origins of microRNA sequencing data
0120
html json tsv all_fa rnatype_unknown_fa versions
miRTrace is a new quality control and taxonomic tracing tool developed specifically for small RNA sequencing data (sRNA-Seq). Each sample is characterized by profiling sequencing quality, read length, sequencing depth and miRNA complexity and also the amounts of miRNAs versus undesirable sequences (derived from tRNAs, rRNAs and sequencing artifacts). In addition to these routine quality control (QC) analyses, miRTrace can accurately and sensitively resolve taxonomic origins of small RNA-Seq data based on the composition of clade-specific miRNAs. This feature can be used to detect cross-clade contaminations in typical lab settings. It can also be applied for more specific applications in forensics, food quality control and clinical diagnosis, for instance tracing the origins of meat products or detecting parasitic microRNAs in host serum.
Download a mitochondrial genome to be used as reference for MitoHiFi
01
fasta gb versions
Fetch mitochondrial genome in Fasta and Genbank format from NCBI
A python workflow that assembles mitogenomes from Pacbio HiFi reads
010000
fasta stats gb gff all_potential_contigs contigs_annotations contigs_circularization contigs_filtering coverage_mapping coverage_plot final_mitogenome_annotation final_mitogenome_choice final_mitogenome_coverage potential_contigs reads_mapping_and_assembly shared_genes versions
A python workflow that assembles mitogenomes from Pacbio HiFi reads
Cluster sequences using MMSeqs2 cluster.
01
db_cluster versions
MMseqs2: ultra fast and sensitive sequence search and clustering suite
Create an MMseqs database from an existing FASTA/Q file
01
db versions
MMseqs2: ultra fast and sensitive sequence search and clustering suite
Creates sequence index for mmseqs database
01
db_indexed versions
MMseqs2: ultra fast and sensitive sequence search and clustering suite
Create a tsv file from a query and a target database as well as the result database
010101
tsv versions
MMseqs2: ultra fast and sensitive sequence search and clustering suite
Download an mmseqs-formatted database
0
database versions
MMseqs2: ultra fast and sensitive sequence search and clustering suite
Searches for the sequences of a fasta file in a database using MMseqs2
0101
tsv versions
MMseqs2: ultra fast and sensitive sequence search and clustering suite
Cluster sequences in linear time using MMSeqs2 linclust.
01
db_cluster versions
MMseqs2: ultra fast and sensitive sequence search and clustering suite
Search and calculate a score for similar sequences in a query and a target database.
0101
db_search versions
MMseqs2: ultra fast and sensitive sequence search and clustering suite
Computes the lowest common ancestor by identifying the query sequence homologs against the target database.
010
db_taxonomy versions
MMseqs2: ultra fast and sensitive sequence search and clustering suite
Conversion of expandable profile to databases to the MMseqs2 databases format
0
db_exprofile versions
MMseqs2: ultra fast and sensitive sequence search and clustering suite
A tool to reconstruct plasmids in bacterial assemblies
01
chromosome contig_report plasmids mobtyper_results versions
Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.
A bioinformatics tool for working with modified bases
0120101
bed bedgraph log versions
A bioinformatics tool for working with modified bases in Oxford Nanopore sequencing data
Contrast-limited adjusted histogram equalization (CLAHE) on single-channel tif images.
01
img_clahe versions
One-stop-shop for scripts and tools for processing data for molkart and spatial omics pipelines.
Download the mOTUs database
0
db versions
The mOTU profiler is a computational tool that estimates relative taxonomic abundance of known and currently unknown microbial community members using metagenomic shotgun sequencing data.
Taxonomic meta-omics profiling using universal marker genes
0100
txt biom versions
Marker gene-based OTU (mOTU) profiling
Taxonomic meta-omics profiling using universal marker genes
010
out versions
Marker gene-based operational taxonomic unit (mOTU) profiling
Taxonomic meta-omics profiling using universal marker genes
010
out bam mgc log versions
Marker gene-based OTU (mOTU) profiling
Evaluate microsattelite instability (MSI) using paired tumor-normal sequencing data
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output output_dis output_germline output_somatic versions
MSIsensor is a C++ program to detect replication slippage variants at microsatellite regions, and differentiate them as somatic or germline.
Scan a reference genome to get microsatellite & homopolymer information
01
txt versions
MSIsensor is a C++ program to detect replication slippage variants at microsatellite regions, and differentiate them as somatic or germline.
msisensor2 detection of MSI regions.
01234500
msi distribution somatic versions
MSIsensor2 is a novel algorithm based machine learning, featuring a large upgrade in the microsatellite instability (MSI) detection for tumor only sequencing data, including Cell-Free DNA (cfDNA), Formalin-Fixed Paraffin-Embedded(FFPE) and other sample types. The original MSIsensor is specially designed for tumor/normal paired sequencing data.
msisensor2 detection of MSI regions.
00
scan versions
MSIsensor2 is a novel algorithm based machine learning, featuring a large upgrade in the microsatellite instability (MSI) detection for tumor only sequencing data, including Cell-Free DNA (cfDNA), Formalin-Fixed Paraffin-Embedded(FFPE) and other sample types. The original MSIsensor is specially designed for tumor/normal paired sequencing data.
MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients with next generation sequencing data. It accepts the whole genome sequencing, whole exome sequencing and target region (panel) sequencing data as input
01234500
output_report output_dis output_germline output_somatic versions
Microsatellite Instability (MSI) detection using high-throughput sequencing data.
MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients with next generation sequencing data. It accepts the whole genome sequencing, whole exome sequencing and target region (panel) sequencing data as input
01
list versions
Microsatellite Instability (MSI) detection using high-throughput sequencing data.
Aligns protein structures using mTM-align
010
alignment structure versions
Algorithm for structural multiple sequence alignments
Parallel implementation of the gzip algorithm.
A small Java tool to calculate ratios between MT and nuclear sequencing reads in a given BAM file.
010
mtnucratio json versions
Convert genomic BAM/SAM files to transcriptomic BAM/RAD files.
01000
bam rad versions
mudskipper is a tool for converting genomic BAM/SAM files to transcriptomic BAM/RAD files.
Build and store a gtf index, which is useful for converting genomic BAM/SAM files to transcriptomic BAM/SAM files.
0
index versions
mudskipper is a tool for converting genomic BAM/SAM files to transcriptomic BAM/RAD files.
Aggregate results from bioinformatics analyses across many samples into a single report
000000
report data plots versions
MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
SNP table generator from GATK UnifiedGenotyper with functionality geared for aDNA
010101010000001
full_alignment info_txt snp_alignment snp_genome_alignment snpstatistics snptable snptable_snpeff snptable_uncertainty structure_genotypes structure_genotypes_nomissing json versions
MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. A range of options are provided that give you the choice of optimizing accuracy, speed, or some compromise between the two
01
aligned_fasta phyi phys clustalw html msf tree log versions
Muscle is a program for creating multiple alignments of amino acid or nucleotide sequences. This particular module uses the super5 algorithm for very big alignments. It can permutate the guide tree according to a set of flags.
010
alignment versions
Muscle v5 is a major re-write of MUSCLE based on new algorithms.
Parallel implementation of the gzip algorithm.
AMR predictions for supported species
010
csv json versions
Antibiotic resistance prediction in minutes
NACHO (NAnostring quality Control dasHbOard) is developed for NanoString nCounter data. NanoString nCounter data is a messenger-RNA/micro-RNA (mRNA/miRNA) expression assay and works with fluorescent barcodes. Each barcode is assigned a mRNA/miRNA, which can be counted after bonding with its target. As a result each count of a specific barcode represents the presence of its target mRNA/miRNA.
0101
normalized_counts normalized_counts_wo_HK versions
R package that uses two main functions to summarize and visualize NanoString RCC files,
namely: load_rcc() and visualise(). It also includes a function normalise(), which (re)calculates
sample specific size factors and normalises the data.
For more information vignette("NACHO") and vignette("NACHO-analysis")
NACHO (NAnostring quality Control dasHbOard) is developed for NanoString nCounter data. NanoString nCounter data is a messenger-RNA/micro-RNA (mRNA/miRNA) expression assay and works with fluorescent barcodes. Each barcode is assigned a mRNA/miRNA, which can be counted after bonding with its target. As a result each count of a specific barcode represents the presence of its target mRNA/miRNA.
0101
nacho_qc_reports nacho_qc_png nacho_qc_txt versions
R package that uses two main functions to summarize and visualize NanoString RCC files,
namely: load_rcc() and visualise(). It also includes a function normalise(), which (re)calculates
sample specific size factors and normalises the data.
For more information vignette("NACHO") and vignette("NACHO-analysis")
Compare multiple runs of long read sequencing data and alignments
01
report_html lengths_violin_html log_length_violin_html n50_html number_of_reads_html overlay_histogram_html overlay_histogram_normalized_html overlay_log_histogram_html overlay_log_histogram_normalized_html total_throughput_html quals_violin_html overlay_histogram_identity_html overlay_histogram_phredscore_html percent_identity_violin_html active_pores_over_time_html cumulative_yield_plot_gigabases_html sequencing_speed_over_time_html stats_txt versions
Parse all the supporting reads of putative somatic SVs using nanomonsv. After successful completion, you will find supporting reads stratified by deletions, insertions, and rearrangements. A precursor to "nanomonsv get"
012
insertions insertions_index deletions deletions_index rearrangements rearrangements_index bp_info bp_info_index versions
nanomonsv is a software for detecting somatic structural variations from paired (tumor and matched control) cancer genome sequence data.
Run NanoPlot on nanopore-sequenced reads
01
html png txt log versions
Nanoq implements ultra-fast read filters and summary reports for high-throughput nanopore reads.
010
stats reads versions
Create DRAGEN hashtable for reference genome
01
hashmap versions
narfmap is a fork of the Dragen mapper/aligner Open Source Software.
A tool to quickly download assemblies from NCBI's Assembly database
0000
gbk fna rm features gff faa gpff wgs_gbk cds rna rna_fna report stats versions
NCBI tool for detecting vector contamination in nucleic acid sequences. This tool is older than NCBI's FCS-adaptor, which is for the same purpose
0101
vecscreen_output versions
"NCBI libraries for biology applications (text-based utilities)"
Get dataset for SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (C++ implementation)
00
dataset versions
SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks
SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (C++ implementation)
010
csv csv_errors csv_insertions tsv json json_auspice ndjson fasta_aligned fasta_translation nwk versions
SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks
Performs fastq alignment to a fasta reference using NextGenMap
010
bam versions
NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime
Serotyping Neisseria gonorrhoeae assemblies
01
tsv versions
Merging paired-end reads and removing sequencing adapters.
01
merged_reads unstitched_read1 unstitched_read2 versions
Determines the gender of a sample from the BAM/CRAM file.
01201010
tsv versions
Short-read sequencing tools
Determining whether sequencing data comes from the same individual by using SNP matching. This module generates vaf files for individual fastq file(s), ready for the vafncm module.
0101
vaf versions
NGSCheckMate is a software package for identifying next generation sequencing (NGS) data files from the same individual, including matching between DNA and RNA.
Determining whether sequencing data comes from the same individual by using SNP matching. Designed for humans on vcf or bam files.
010101
corr_matrix matched all pdf vcf versions
NGSCheckMate is a software package for identifying next generation sequencing (NGS) data files from the same individual, including matching between DNA and RNA.
Determining whether sequencing data comes from the same individual by using SNP matching. This module generates PT files from a bed file containing individual positions.
010101
pt versions
NGSCheckMate is a software package for identifying next generation sequencing (NGS) data files from the same individual, including matching between DNA and RNA.
Determining whether sequencing data comes from the same individual by using SNP matching. This module generates PT files from a bed file containing individual positions.
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pdf corr_matrix all matched versions
NGSCheckMate is a software package for identifying next generation sequencing (NGS) data files from the same individual, including matching between DNA and RNA.
write your description here
metareadsformatmode
meta versions npa npc npl npo
Visualise metagenome redundancy curve in PNG format from a single Nonpareil npo file
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png versions
Estimate average coverage and create curves for metagenomic datasets
Calculate metagenome redundancy curve from FASTQ files
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npa npc npl npo versions
Estimate average coverage and create curves for metagenomic datasets
Generate summary reports with raw data for Nonpareil NPO curves, including MultiQC compatible JSON/TSV files
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json tsv csv pdf versions
Estimate average coverage and create curves for metagenomic datasets
Visualise metagenome redundancy curves in PNG format from multiple Nonpareil npo files in a single image
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png versions
Estimate average coverage and create curves for metagenomic datasets
NUCmer is a pipeline for the alignment of multiple closely related nucleotide sequences.
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delta coords versions
Construct a dynamic succinct variation graph in ODGI format from a GFAv1.
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og versions
An optimized dynamic genome/graph implementation
Draw previously-determined 2D layouts of the graph with diverse annotations.
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png versions
An optimized dynamic genome/graph implementation
Establish 2D layouts of the graph using path-guided stochastic gradient descent. The graph must be sorted and id-compacted.
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lay tsv versions
An optimized dynamic genome/graph implementation
Apply different kind of sorting algorithms to a graph. The most prominent one is the PG-SGD sorting algorithm.
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sorted_graph versions
An optimized dynamic genome/graph implementation
Squeezes multiple graphs in ODGI format into the same file in ODGI format.
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graph versions
An optimized dynamic genome/graph implementation
Metrics describing a variation graph and its path relationship.
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tsv yaml versions
An optimized dynamic genome/graph implementation
Merge unitigs into a single node preserving the node order.
01
unchopped_graph versions
An optimized dynamic genome/graph implementation
Project a graph into other formats.
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gfa versions
An optimized dynamic genome/graph implementation
Visualize a variation graph in 1D.
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png versions
An optimized dynamic genome/graph implementation
Calls CNVs in bam files from tumor patients
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png profile summary versions
Create a decoy peptide database from a standard FASTA database.
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decoy_fasta versions
OpenMS is an open-source software C++ library for LC-MS data management and analyses
Filters peptide/protein identification results by different criteria.
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mzml featurexml consensusxml versions
OpenMS is an open-source software C++ library for LC-MS data management and analyses
Filters peptide/protein identification results by different criteria.
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filtered versions
OpenMS is an open-source software C++ library for LC-MS data management and analyses
Calculates a distribution of the mass error from given mass spectra and IDs.
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frag_err prec_err versions
OpenMS is an open-source software C++ library for LC-MS data management and analyses
Merges several idXML files into one idXML file.
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idxml versions
OpenMS is an open-source software C++ library for LC-MS data management and analyses
Split a merged identification file into their originating identification files
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idxmls versions
OpenMS is an open-source software C++ library for LC-MS data management and analyses
Switches between different scores of peptide or protein hits in identification data
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idxml versions
OpenMS is an open-source software C++ library for LC-MS data management and analyses
A tool for peak detection in high-resolution profile data (Orbitrap or FTICR)
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mzml versions
OpenMS is an open-source software C++ library for LC-MS data management and analyses
Refreshes the protein references for all peptide hits.
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indexed_idxml versions
OpenMS is an open-source software C++ library for LC-MS data management and analyses
Annotates MS/MS spectra using Comet.
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idxml pin versions
OpenMS is an open-source software C++ library for LC-MS data management and analyses
Perform HLA-I typing of sequencing data
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hla_type coverage_plot versions
OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics.
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orthofinder working versions
A program to convert bam into paf.
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paf versions
A program to manipulate paf files / convert to and from paf.
a tool for indexing and querying on a block-compressed text file containing pairs of genomic coordinates
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index versions
Find and remove PCR/optical duplicates
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pairs stat versions
CLI tools to process mapped Hi-C data
Flip pairs to get an upper-triangular matrix
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flip versions
CLI tools to process mapped Hi-C data
Merge multiple pairs/pairsam files
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pairs versions
CLI tools to process mapped Hi-C data
Find ligation junctions in .sam, make .pairs
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pairsam stat versions
CLI tools to process mapped Hi-C data
Assign restriction fragments to pairs
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restrict versions
CLI tools to process mapped Hi-C data
Select pairs according to given condition by options.args
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selected unselected versions
CLI tools to process mapped Hi-C data
Sort a .pairs/.pairsam file
01
sorted versions
CLI tools to process mapped Hi-C data
Split a .pairsam file into .pairs and .sam.
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pairs bam versions
CLI tools to process mapped Hi-C data
Calculate pairs statistics
01
stats versions
CLI tools to process mapped Hi-C data
Calculates a coverage histogram from a GFA file and constructs a growth table from this as either a TSV or HTML file
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tsv versions
panacus is a tool for computing counting statistics for GFA files
Create visualizations from a tsv coverage histogram created with panacus.
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image versions
panacus is a tool for computing counting statistics for GFA files
A fast and scalable tool for bacterial pangenome analysis
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results aln versions
panaroo - an updated pipeline for pangenome investigation
Phylogenetic Assignment of Named Global Outbreak LINeages
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report versions
Phylogenetic Assignment of Named Global Outbreak LINeages
Phylogenetic Assignment of Named Global Outbreak LINeages
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db versions
Phylogenetic Assignment of Named Global Outbreak LINeages
NVIDIA Clara Parabricks GPU-accelerated apply Base Quality Score Recalibration (BQSR).
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bam bai versions
NVIDIA Clara Parabricks GPU-accelerated genomics tools
NVIDIA Clara Parabricks GPU-accelerated variant calls annotation based on dbSNP database
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vcf versions
NVIDIA Clara Parabricks GPU-accelerated genomics tools
NVIDIA Clara Parabricks GPU-accelerated germline variant calling, replicating deepvariant.
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vcf gvcf versions
NVIDIA Clara Parabricks GPU-accelerated genomics tools
NVIDIA Clara Parabricks GPU-accelerated alignment, sorting, BQSR calculation, and duplicate marking. Note this nf-core module requires files to be copied into the working directory and not symlinked.
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bam bai cram crai bqsr_table qc_metrics duplicate_metrics versions
NVIDIA Clara Parabricks GPU-accelerated genomics tools
VIDIA Clara Parabricks GPU-accelerated fast, accurate algorithm for mapping methylated DNA sequence reads to a reference genome, performing local alignment, and producing alignment for different parts of the query sequence
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bam bai qc_metrics bqsr_table duplicate_metrics versions
NVIDIA Clara Parabricks GPU-accelerated genomics tools
NVIDIA Clara Parabricks GPU-accelerated joint genotyping, replicating GATK GenotypeGVCFs
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vcf versions
NVIDIA Clara Parabricks GPU-accelerated genomics tools
NVIDIA Clara Parabricks GPU-accelerated germline variant calling, replicating GATK haplotypecaller.
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vcf gvcf versions
NVIDIA Clara Parabricks GPU-accelerated genomics tools
NVIDIA Clara Parabricks GPU-accelerated gvcf indexing tool.
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gvcf_index versions
NVIDIA Clara Parabricks GPU-accelerated genomics tools
Determines the depth in a BAM/CRAM file
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depth binned_depth versions
Graph realignment tools for structural variants
Genotype structural variants using paragraph and grmpy
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vcf json versions
Graph realignment tools for structural variants
Convert a VCF file to a JSON graph
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graph versions
Graph realignment tools for structural variants
The pbbam software package provides components to create, query, & edit PacBio BAM files and associated indices. These components include a core C++ library, bindings for additional languages, and command-line utilities.
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bam pbi versions
PacBio BAM C++ library
Alignment with PacBio's minimap2 frontend
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bam versions
A minimap2 frontend for PacBio native data formats
pbsv - PacBio structural variant (SV) signature discovery tool
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svsig versions
pbsv - PacBio structural variant (SV) calling and analysis tools
converts pacbio bam files to fastq.gz using PacBioToolKit (pbtk) bam2fastq
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fastq versions
pbtk - PacBio BAM toolkit
Minimalistic tool which creates an index file that enables random access into PacBio BAM files
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pbi versions
pbtk - PacBio BAM toolkit
"This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays."
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spp pdf rdata versions
Predict prophages in bacterial genomes
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coordinates gbk log information bacteria_fasta bacteria_gbk phage_fasta phage_gbk prophage_gff prophage_tbl prophage_tsv versions
Prophage finder using multiple metrics
phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
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results versions
Assigns all the reads in a file to a single new read-group
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bam bai cram versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Creates an interval list from a bed file and a reference dict
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interval_list versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Cleans the provided BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads
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bam versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Collects hybrid-selection (HS) metrics for a SAM or BAM file.
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metrics versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Collect metrics about the insert size distribution of a paired-end library.
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metrics histogram versions
Java tools for working with NGS data in the BAM format
Collect multiple metrics from a BAM file
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metrics pdf versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Collect metrics from a RNAseq BAM file
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metrics pdf versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments.
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metrics versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Creates a sequence dictionary for a reference sequence.
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reference_dict versions
Creates a sequence dictionary file (with ".dict" extension) from a reference sequence provided in FASTA format, which is required by many processing and analysis tools. The output file contains a header but no SAMRecords, and the header contains only sequence records.
Checks that all data in the set of input files appear to come from the same individual
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crosscheck_metrics versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Computes/Extracts the fingerprint genotype likelihoods from the supplied file. It is given as a list of PLs at the fingerprinting sites.
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vcf tbi versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Converts a FASTQ file to an unaligned BAM or SAM file.
01
bam versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Filters SAM/BAM files to include/exclude either aligned/unaligned reads or based on a read list
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bam versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Verify mate-pair information between mates and fix if needed
01
bam versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Lifts over a VCF file from one reference build to another.
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vcf_lifted vcf_unlifted versions
Move annotations from one assembly to another
Locate and tag duplicate reads in a BAM file
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bam bai cram metrics versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Merges multiple BAM files into a single file
01
bam versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Samples a SAM/BAM/CRAM file using flowcell position information for the best approximation of having sequenced fewer reads
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bam bai num_reads versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
changes name of sample in the vcf file
01
vcf versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Writes an interval list created by splitting a reference at Ns.A Program for breaking up a reference into intervals of alternating regions of N and ACGT bases
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intervals versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
This tool takes in a coordinate-sorted SAM or BAM and calculatesthe NM, MD, and UQ tags by comparing with the reference.
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bam bai versions
Java tools for working with NGS data in the BAM format
Sorts BAM/SAM files based on a variety of picard specific criteria
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bam versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Sorts vcf files
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vcf versions
Java tools for working with NGS data in the BAM/CRAM/SAM and VCF format
Compresses files with pigz.
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archive versions
Parallel implementation of the gzip algorithm.
write your description here
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file versions
Parallel implementation of the gzip algorithm.
Automatically improve draft assemblies and find variation among strains, including large event detection
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improved_assembly vcf change_record tracks_bed tracks_wig versions
Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data
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bp cem del dd int_final inv li rp si td versions
Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data
Main caller script for peak calling
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divergent_TREs bidirectional_TREs unidirectional_TREs peakcalling_log versions
Peak Identifier for Nascent Transcripts Starts (PINTS)
Identify plasmids in bacterial sequences and assemblies
01
json txt tsv genome_seq plasmid_seq versions
Epistasis in PLINK, analyzing how the effects of one gene depend on the presence of others.
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epi episummary log nosex versions
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
Exclude variant identifiers from plink bfiles
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bed bim fam versions
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
Subset plink bfiles with a text file of variant identifiers
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bed bim fam versions
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
Fast Epistasis in PLINK, analyzing how the effects of one gene depend on the presence of others.
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fepi fepisummary flog fnosex versions
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
Calculates identity-by-descent over autosomal SNPs
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genome versions
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
Generate GWAS association studies
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assoc log nosex versions
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
Generate Hardy-Weinberg statistics for provided input
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hwe versions
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
Produce a pruned subset of markers that are in approximate linkage equilibrium with each other.
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prunein pruneout versions
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
Produce a pruned subset of markers that are in approximate linkage equilibrium with each other. Pairs of variants in the current window with squared correlation greater than the threshold are noted and variants are greedily pruned from the window until no such pairs remain.
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prunein pruneout versions
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
LD analysis in PLINK examines genetic variant associations within populations
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ld log nosex versions
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
Recodes plink bfiles into a new text fileset applying different modifiers
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ped map txt raw traw beagledat chrdat chrmap geno pheno pos phase info lgen list gen gengz sample rlist strctin tped tfam vcf vcfgz versions
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
Subset plink pfiles with a text file of variant identifiers
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extract_pgen extract_psam extract_pvar versions
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner
Calculate Inbreeding data with plink2
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het versions
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner
Produce pruned set of variants in approximatelinkage equilibrium
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prune_in prune_out versions
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner
Perform PCA analysis using PLINK
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evecfile evfile logfile versions
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner
Remove samples from a plink2 dataset
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remove_bim remove_bed remove_fam remove_pgen remove_psam remove_pvar versions
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner
Apply a scoring system to each sample in a plink 2 fileset
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score versions
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner
Import variant genetic data using plink2
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pgen psam pvar pvar_zst versions
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner
Convert from VCF file to BGEN file version 1.2 format preserving dosages.
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bgen_file sample_file log_file versions
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner
pmdtools command to filter ancient DNA molecules from others
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bam versions
Compute postmortem damage patterns and decontaminate ancient genomes
Determine Streptococcus pneumoniae serotype from Illumina paired-end reads
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xml txt versions
Polishing genome assemblies with short reads.
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fasta versions debug
Polishing genome assemblies with short reads.
PoolSNP is a heuristic SNP caller, which uses an MPILEUP file and a reference genome in FASTA format as inputs.
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vcf max_cov bad_sites versions
Software to deconvolute sample identity and identify multiplets when multiple samples are pooled by barcoded single cell sequencing and external genotyping data for each sample is available.
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demuxlet_result versions
A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxiliary tools
Software to pileup reads and corresponding base quality for each overlapping SNPs and each barcode.
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cel plp var umi versions
A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxiliary tools
Software to deconvolute sample identity and identify multiplets when multiple samples are pooled by barcoded single cell sequencing and external genotyping data for each sample is not available.
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result vcf lmix singlet_result singlet_vcf versions
A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxiliary tools
Extension of Porechop whose purpose is to process adapter sequences in ONT reads.
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reads log versions
Adapter removal and demultiplexing of Oxford Nanopore reads
01
reads log versions
Adapter removal and demultiplexing of Oxford Nanopore reads
Run all Portcullis steps in one go
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log pass_junctions_bed pass_junctions_tab intron_gff exon_gff spliced_bam spliced_bai versions
Portcullis is a tool that filters out invalid splice junctions from RNA-seq alignment data. It accepts BAM files from various RNA-seq mappers, analyzes splice junctions and removes likely false positives, outputting filtered results in multiple formats for downstream analysis.
Software for predicting library complexity and genome coverage in high-throughput sequencing
01
c_curve log versions
Software for predicting library complexity and genome coverage in high-throughput sequencing
Software for predicting library complexity and genome coverage in high-throughput sequencing
01
lc_extrap log versions
Software for predicting library complexity and genome coverage in high-throughput sequencing
Calculate pairwise nucleotide identity with respect to a reference sequence
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valid_fasta invalid_fasta report log versions
Filter reads by quality score.
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reads logs versions log_tab
A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.
converts sam/bam/cram/pairs into genome contact map
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pretext versions
a module to generate images from Pretext contact maps.
01
image versions
PRINSEQ++ is a C++ implementation of the prinseq-lite.pl program. It can be used to filter, reformat or trim genomic and metagenomic sequence data
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good_reads single_reads bad_reads log versions
Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program
010
gene_annotations nucleotide_fasta amino_acid_fasta all_gene_annotations versions
Whole genome annotation of small genomes (bacterial, archeal, viral)
0100
gff gbk fna faa ffn sqn fsa tbl err log txt tsv versions
frame-shift correction for long read (meta)genomics - fix frameshifts in reads
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out_fa versions
frame-shift correction for long read (meta)genomics
frame-shift correction for long read (meta)genomics - maps proteins to reads
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tsv versions
frame-shift correction for long read (meta)genomics
Perform Gene Ratio Enrichment Analysis
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results versions session_info
Gene Ratio Enrichment Analysis
Transform the data matrix using centered logratio transformation (CLR) or additive logratio transformation (ALR)
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logratio session_info versions
Logratio methods for omics data
Perform differential proportionality analysis
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results_genewise genewise_plot rdata results_pairwise results_pairwise_filtered adjacency fdr session_info versions
Logratio methods for omics data
Perform logratio-based correlation analysis -> get proportionality & basis shrinkage partial correlation coefficients. One can also compute standard correlation coefficients, if required.
01
propr matrix fdr adj warnings session_info versions
Logratio methods for omics data
Efficient Estimation of Covariance and (Partial) Correlation
Proteinortho is a tool to detect orthologous genes within different species.
01
orthologgroups orthologgraph blastgraph versions
reads a maxQuant proteinGroups file with Proteus
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dendro_plot mean_var_plot raw_dist_plot norm_dist_plot raw_rdata norm_rdata raw_tab norm_tab session_info versions
R package for analysing proteomics data
Calculate intervals coverage for each sample. N.B. the tool can not handle staging files with symlinks, stageInMode should be set to 'link'.
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txt png loess_qc_txt loess_txt versions
Copy number calling and SNV classification using targeted short read sequencing
Generate on and off-target intervals for PureCN from a list of targets
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txt bed versions
Copy number calling and SNV classification using targeted short read sequencing
Build a normal database for coverage normalization from all the (GC-normalized) normal coverage files. N.B. as reported in https://www.bioconductor.org/packages/devel/bioc/vignettes/PureCN/inst/doc/Quick.html, it is advised to provide a normal panel (VCF format) to precompute mapping bias for faster runtimes.
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rds png bias_rds bias_bed low_cov_bed versions
Copy number calling and SNV classification using targeted short read sequencing
Run PureCN workflow to normalize, segment and determine purity and ploidy
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pdf local_optima_pdf seg genes_csv amplification_pvalues_csv vcf_gz variants_csv loh_csv chr_pdf segmentation_pdf multisample_seg versions
Copy number calling and SNV classification using targeted short read sequencing
Calculate coverage cutoffs to determine when to purge duplicated sequence.
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cutoff log versions
Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth
Separates out sequences purged of falsely duplicated sequences.
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haplotigs purged versions
Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth
Plots the read coverage from a purge dups statistics file and cutoffs.
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png versions
Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth
Create read depth histogram and base-level read depth for an assembly based on pacbio data
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stat basecov versions
Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth
Purge haplotigs and overlaps for an assembly
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bed log versions
Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth
Split fasta file by 'N's to aid in self alignment for duplicate purging
01
split_fasta versions
Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth
Damage parameter estimation for ancient DNA
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csv versions
Damage parameter estimation for ancient DNA
Damage parameter estimation for ancient DNA
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csv versions
Damage parameter estimation for ancient DNA
Compute summary statistics for control gene from BAM files.
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control_stats versions
A Python package for pharmacogenomics research
Call SNVs/indels from BAM files for all target genes.
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vcf tbi versions
A Python package for pharmacogenomics research
Prepare a depth of coverage file for all target genes with SV from BAM files.
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coverage versions
A Python package for pharmacogenomics research
PyPGx pharmacogenomics genotyping pipeline for NGS data.
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results cnv_calls consolidated_variants versions
A Python package for pharmacogenomics research
Pyrodigal is a Python module that provides bindings to Prodigal, a fast, reliable protein-coding gene prediction for prokaryotic genomes.
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annotations fna faa score versions
Evaluate alignment data
010
results versions
Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Interface and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.
Evaluate alignment data
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results versions
Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Interface and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.
Evaluate alignment data
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results versions
Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Interface and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.
QUILT is an R and C++ program for rapid genotype imputation from low-coverage sequence using a large reference panel.
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vcf tbi rdata plots versions
Read aware low coverage whole genome sequence imputation from a reference panel
Produces a Newick format phylogeny from a multiple sequence alignment using a Neighbour-Joining algorithm. Capable of bacterial genome size alignments.
0
stockholm_alignment phylogeny versions
Randomly subsample sequencing reads to a specified coverage
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reads versions
De novo genome assembler for long uncorrected reads.
01
fasta gfa versions
RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion.
0
phylogeny phylogeny_bootstrapped versions
Extract exon-exon junctions from an RNAseq BAM file. The output is a BED file in the BED12 format.
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junc versions
RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context.
Screening DNA sequences for interspersed repeats and low complexity DNA sequences
010
masked out tbl gff versions
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences
Create a database for RepeatModeler
01
db versions
RepeatModeler is a de-novo repeat family identification and modeling package.
Performs de novo transposable element (TE) family identification with RepeatModeler
01
fasta stk log versions
RepeatModeler is a de-novo repeat family identification and modeling package.
ResFinder identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria
01200
json disinfinder_kma pheno_table_species pheno_table pointfinder_kma pointfinder_prediction pointfinder_results pointfinder_table resfinder_hit_in_genome_seq resfinder_blast resfinder_kma resfinder_resistance_gene_seq resfinder_results_table resfinder_results_tab resfinder_results versions
ResFinder identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria
Preprocess the CARD database for RGI to predict antibiotic resistance from protein or nucleotide data
0
db tool_version db_version versions
This module preprocesses the downloaded Comprehensive Antibiotic Resistance Database (CARD) which can then be used as input for RGI.
Predict antibiotic resistance from protein or nucleotide data
0100
json tsv tmp tool_version db_version versions
This tool provides a preliminary annotation of your DNA sequence(s) based upon the data available in The Comprehensive Antibiotic Resistance Database (CARD). Hits to genes tagged with Antibiotic Resistance ontology terms will be highlighted. As CARD expands to include more pathogens, genomes, plasmids, and ontology terms this tool will grow increasingly powerful in providing first-pass detection of antibiotic resistance associated genes. See license at CARD website
Markup VCF file using rho-calls.
012010
vcf versions
Call regions of homozygosity and make tentative UPD calls.
Call regions of homozygosity and make tentative UPD calls
0101
bed wig versions
Call regions of homozygosity and make tentative UPD calls.
Quality control of riboseq bam data
012012012010101
predictions all transprofile versions
Ribo TIS Hunter (Ribo-TISH) identifies translation activities using ribosome profiling data.
Quality control of riboseq bam data
01201
distribution pdf offset versions
Ribo TIS Hunter (Ribo-TISH) identifies translation activities using ribosome profiling data.
Accurate detection of short and long active ORFs using Ribo-seq data
01201
protocol bam_summary read_length_dist metagene_profile_5p metagene_profile_3p metagene_plots psite_offsets pos_wig neg_wig orfs versions
Python package to detect translating ORF from Ribo-seq data
Accurate detection of short and long active ORFs using Ribo-seq data
012
candidate_orfs versions
Python package to detect translating ORF from Ribo-seq data
Render an rmarkdown notebook. Supports parametrization.
0100
report parameterised_notebook artifacts session_info versions
Dynamic Documents for R
Calculate pan-genome from annotated bacterial assemblies in GFF3 format
01
results aln versions
Ribosomal RNA extraction from a GTF file.
0
rrna_gtf versions
Calculate expression with RSEM
010
counts_gene counts_transcript stat logs versions bam_star bam_genome bam_transcript
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
Prepare a reference genome for RSEM
00
index transcript_fasta versions
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
Generate statistics from a bam file
01
txt versions
RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data.
Infer strandedness from sequencing reads
010
txt versions
RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data.
Calculate inner distance between read pairs.
010
distance freq mean pdf rscript versions
RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data.
compare detected splice junctions to reference gene model
010
xls rscript log bed interact_bed pdf events_pdf versions
RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data.
compare detected splice junctions to reference gene model
010
pdf rscript versions
RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data.
Calculate how mapped reads are distributed over genomic features
010
txt versions
RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data.
Calculate read duplication rate
01
seq_xls pos_xls pdf rscript versions
RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data.
Calculate TIN (transcript integrity number) from RNA-seq reads
0120
txt xls versions
RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data.
Converts a PED file to VCF headers
01
output versions
RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation
Plot ROC curves from vcfeval ROC data files, either to an image, or an interactive GUI. The interactive GUI isn't possible for nextflow.
01
png svg versions
RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation
The VCFeval tool of RTG tools. It is used to evaluate called variants for agreement with a baseline variant set
012345601
tp_vcf tp_tbi fn_vcf fn_tbi fp_vcf fp_tbi baseline_vcf baseline_tbi snp_roc non_snp_roc weighted_roc summary phasing versions
RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation
Uses the RTN R package for transcriptional regulatory network inference (TNI).
01
tni tni_perm tni_bootstrap tni_filtered versions
RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons
sage is a search software for proteomics data
010101
results_tsv results_json results_pin versions tmt_tsv lfq_tsv
Proteomics searching so fast it feels like magic.
Create index for salmon
00
index versions
Salmon is a tool for wicked-fast transcript quantification from RNA-seq data
gene/transcript quantification with Salmon
0100000
results json_info lib_format_counts versions
Salmon is a tool for wicked-fast transcript quantification from RNA-seq data
SALSA, A tool to scaffold long read assemblies with HiC
0120000
fasta agp agp_original_coordinates versions
Calling lowest common ancestors from multi-mapped reads in SAM/BAM/CRAM files
0120
csv json bam versions
Lowest Common Ancestor on SAM/BAM/CRAM alignment files
Outputs some statistics drawn from read flags.
01
stats versions
Tools for working with SAM/BAM data
find and mark duplicate reads in BAM file
01
bam bai versions
process your BAM data faster!
This module combines samtools and samblaster in order to use samblaster capability to filter or tag SAM files, with the advantage of maintaining both input and output in BAM format. Samblaster input must contain a sequence header: for this reason it has been piped with the "samtools view -h" command. Additional desired arguments for samtools can be passed using: options.args2 for the input bam file options.args3 for the output bam file
01
bam versions
Module to validate illuminaยฎ Sample Sheet v2 files.
010
samplesheet versions
Clips read alignments where they match BED file defined regions
01000
bam stats rejects_bam versions
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
The module uses bam2fq method from samtools to convert a SAM, BAM or CRAM file to FASTQ format
010
reads versions
Tools for dealing with SAM, BAM and CRAM files
calculates MD and NM tags
0101
bam versions
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
Concatenate BAM or CRAM file
01
bam cram versions
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
shuffles and groups reads together by their names
0101
bam cram sam versions
Tools for dealing with SAM, BAM and CRAM files
The module uses collate and then fastq methods from samtools to convert a SAM, BAM or CRAM file to FASTQ format
01010
fastq fastq_interleaved fastq_other fastq_singleton versions
Tools for dealing with SAM, BAM and CRAM files
Produces a consensus FASTA/FASTQ/PILEUP
01
fasta fastq pileup versions
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
convert and then index CRAM -> BAM or BAM -> CRAM file
0120101
bam cram bai crai versions
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
produces a histogram or table of coverage per chromosome
0120101
coverage versions
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
List CRAM Content-ID and Data-Series sizes
01
size versions
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
Computes the depth at each position or region.
0101
tsv versions
Tools for dealing with SAM, BAM and CRAM files; samtools depth โ computes the read depth at each position or region
Create a sequence dictionary file from a FASTA file
01
dict versions
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
Index FASTA file, and optionally generate a file of chromosome sizes
01010
fa fai sizes gzi versions
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
Converts a SAM/BAM/CRAM file to FASTA
010
fasta interleaved singleton other versions
Tools for dealing with SAM, BAM and CRAM files
Converts a SAM/BAM/CRAM file to FASTQ
010
fastq interleaved singleton other versions
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
Samtools fixmate is a tool that can fill in information (insert size, cigar, mapq) about paired end reads onto the corresponding other read. Also has options to remove secondary/unmapped alignments and recalculate whether reads are proper pairs.
01
bam cram sam versions
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type
012
flagstat versions
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
filter/convert SAM/BAM/CRAM file
01
readgroup versions
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
Reports alignment summary statistics for a BAM/CRAM/SAM file
012
idxstats versions
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
converts FASTQ files to unmapped SAM/BAM/CRAM
01
sam bam cram versions
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
Index SAM/BAM/CRAM file
01
bai csi crai versions
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
mark duplicate alignments in a coordinate sorted file
0101
bam cram sam versions
Tools for dealing with SAM, BAM and CRAM files
Merge BAM or CRAM file
010101
bam cram csi crai versions
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
BAM
0120
mpileup versions
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
Replace the header in the bam file with the header generated by the command. This command is much faster than replacing the header with a BAMโSAMโBAM conversion.
01
bam versions
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
Collate/Fixmate/Sort/Markdup SAM/BAM/CRAM file
0101
bam cram csi crai metrics versions
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
Sort SAM/BAM/CRAM file
0101
bam cram crai csi versions
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
Produces comprehensive statistics from SAM/BAM/CRAM file
01201
stats versions
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
filter/convert SAM/BAM/CRAM file
0120100
bam cram sam bai csi crai unselected unselected_index versions
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
Module to use scds for doublet scoring
01
rds predictions versions
SCIMAP is a suite of tools that enables spatial single-cell analyses
01
csv h5ad versions
Scimap is a scalable toolkit for analyzing spatial molecular data.
SpatialLDA uses an LDA based approach for the identification of cellular neighborhoods, using cell type identities.
01
spatial_lda_output composition_plot motif_location_plot versions
Scimap is a scalable toolkit for analyzing spatial molecular data. The underlying framework is generalizable to spatial datasets mapped to XY coordinates. The package uses the anndata framework making it easy to integrate with other popular single-cell analysis toolkits. It includes preprocessing, phenotyping, visualization, clustering, spatial analysis and differential spatial testing. The Python-based implementation efficiently deals with large datasets of millions of cells.
The Cluster Analysis tool of Scramble analyses and interprets the soft-clipped clusters found by cluster_identifier
0100
meis_tab dels_tab vcf versions
Soft Clipped Read Alignment Mapper
The cluster_identifier tool of Scramble identifies soft clipped clusters
0120
clusters versions
Soft Clipped Read Alignment Mapper
Module to use scAR to remove ambient RNA from single-cell RNA-seq data
012
h5ad versions
scvi-tools (single-cell variational inference tools) is a package for end-to-end analysis of single-cell omics data
scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics.
Detect doublets in single-cell RNA-Seq data
01
h5ad predictions versions
A scalable toolkit for probabilistic modeling applied to single-cell omics data
Call peaks using SEACR on sequenced reads in bedgraph format
0120
bed versions
SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by "zeroes" (i.e. regions with no read coverage).
A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection
0100
alignment trans_alignments multi_bed single_bed versions
A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection
Generate genome indices for segemehl align
0
index versions
A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection
metagenomic binning with self-supervised learning
012
csv model output_fasta recluster_fasta tsv versions
Metagenomic binning with semi-supervised siamese neural network
Apply a score cutoff to filter variants based on a recalibration table. Sentieon's Aplyvarcal performs the second pass in a two-stage process called Variant Quality Score Recalibration (VQSR). Specifically, it applies filtering to the input variants based on the recalibration table produced in the previous step VarCal and a target sensitivity value. https://support.sentieon.com/manual/usages/general/#applyvarcal-algorithm
0123450101
vcf tbi versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
Create BWA index for reference genome
01
index versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
Performs fastq alignment to a fasta reference using Sentieon's BWA MEM
01010101
bam_and_bai versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
Accelerated implementation of the Picard CollectVariantCallingMetrics tool.
012012010101
metrics summary versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
Accelerated implementation of the GATK DepthOfCoverage tool.
01201010101
per_locus sample_summary statistics coverage_counts coverage_proportions interval_summary versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
Collects multiple quality metrics from a bam file
01201010
mq_metrics qd_metrics gc_summary gc_metrics aln_metrics is_metrics mq_plot qd_plot is_plot gc_plot versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
Runs the sentieon tool LocusCollector followed by Dedup. LocusCollector collects read information that is used by Dedup which in turn marks or removes duplicate reads.
0120101
cram crai bam bai score metrics metrics_multiqc_tsv versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
modifies the input VCF file by adding the MLrejected FILTER to the variants
012010101
vcf index versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
DNAscope algorithm performs an improved version of Haplotype variant calling.
01230101010101000
vcf vcf_tbi gvcf gvcf_tbi versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
Perform joint genotyping on one or more samples pre-called with Sentieon's Haplotyper.
012301010101
vcf_gz vcf_gz_tbi versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
Runs Sentieon's haplotyper for germline variant calling.
012340101010100
vcf vcf_tbi gvcf gvcf_tbi versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
Generate recalibration table and optionally perform base quality recalibration
01201010101010
table table_post recal_alignment csv pdf versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
Merges BAM files, and/or convert them into cram files. Also, outputs the result of applying the Base Quality Score Recalibration to a file.
0120101
output index output_index versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
Filters the raw output of sentieon/tnhaplotyper2.
01234560101
vcf vcf_tbi stats versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
Tnhaplotyper2 performs somatic variant calling on the tumor-normal matched pairs.
01230101010101010100
orientation_data contamination_data contamination_segments stats vcf index versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
TNscope algorithm performs somatic variant calling on the tumor-normal matched pair or the tumor only data, using a Haplotyper algorithm.
012010101201201201
vcf index versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
Module for Sentieons VarCal. The VarCal algorithm calculates the Variant Quality Score Recalibration (VQSR). VarCal builds a recalibration model for scoring variant quality. https://support.sentieon.com/manual/usages/general/#varcal-algorithm
01200000
recal idx tranches plots versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
Collects whole genome quality metrics from a bam file
012010101
wgs_metrics versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
Seqcluster collapse reduces computational complexity by collapsing identical sequences in a FASTQ file.
01
fastq versions
Small RNA analysis from NGS data. Seqcluster generates a list of clusters of small RNA sequences, their genome location, their annotation and the abundance in all the sample of the project.
Dereplicate FASTX sequences, removing duplicate sequences and printing the number of identical sequences in the sequence header. Can dereplicate already dereplicated FASTA files, summing the numbers found in the headers.
01
fasta versions
DNA sequence utilities for FASTX files
Statistics for FASTA or FASTQ files
01
stats multiqc versions
Cross-platform compiled suite of tools to manipulate and inspect FASTA and FASTQ files
Concatenating multiple uncompressed sequence files together
01
fastx versions
Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
Convert FASTQ to FASTA format
01
fasta versions
Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
Select sequences from a large file based on name/ID
010
filter versions
Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
match up paired-end reads from two fastq files
01
reads unpaired_reads versions
Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
Use seqkit to find/replace strings within sequences and sequence headers
01
fastx versions
Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
Transforms sequences (extract ID, filter by length, remove gaps, reverse complement...)
01
fastx log versions
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
Transforms sequences (extract ID, filter by length, remove gaps, reverse complement...)
01
fastx versions
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
Use seqkit to generate sliding windows of input fasta
01
fastx versions
Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
Sorts sequences by id/name/sequence/length
01
fastx versions
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
Split single or paired-end fastq.gz files
01
reads versions
Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
simple statistics of FASTA/Q files
01
stats versions
Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
Translate DNA/RNA to protein sequence
01
fastx versions
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
Salmonella serotype prediction from reads and assemblies
01
log tsv txt versions
Computes sequence statistics from FASTQ or FASTA files
01
seqtk_stats versions
Generates a BED file containing genomic locations of lengths of N.
01
bed versions
Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. Seqtk mergepe command merges pair-end reads into one interleaved file.
Interleave pair-end reads from FastQ files
01
reads versions
Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. Seqtk mergepe command merges pair-end reads into one interleaved file.
Rename sequence names in FASTQ or FASTA files.
01
sequences versions
Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. The seqtk rename command renames sequence names.
Subsample reads from FASTQ files
012
reads versions
Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. Seqtk sample command subsamples sequences.
Common transformation operations on FASTA or FASTQ files.
01
fastx versions
Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. The seqtk seq command enables common transformation operations on FASTA or FASTQ files.
Select only sequences that match the filtering condition
010
sequences versions
Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format
Trim low quality bases from FastQ files
01
reads versions
Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format
Sequence quality metrics for FASTQ and uBAM files.
01
json html versions
PileupCaller is a tool to create genotype calls from bam files using read-sampling methods
0100
eigenstrat plink freqsum versions
Tools for population genetics on sequencing data
Sequenza-utils bam2seqz process BAM and Wiggle files to produce a seqz file
01200
seqz versions
Sequenza-utils provides 3 main command line programs to transform common NGS file format - such as FASTA, BAM - to input files for the Sequenza R package. The program - bam2seqz - process a paired set of BAM/pileup files (tumour and matching normal), and GC-content genome-wide information, to extract the common positions with A and B alleles frequencies.
Sequenza-utils gc_wiggle computes the GC percentage across the sequences, and returns a file in the UCSC wiggle format, given a fasta file and a window size.
01
wig versions
Sequenza-utils provides 3 main command line programs to transform common NGS file format - such as FASTA, BAM - to input files for the Sequenza R package. The program -gc_wiggle- takes fasta file as an input, computes GC percentage across the sequences and returns a file in the UCSC wiggle format.
Induce a variation graph in GFA format from alignments in PAF format
012
gfa versions
seqwish implements a lossless conversion from pairwise alignments between sequences to a variation graph encoding the sequences and their alignments.
Determine Streptococcus pneumoniae serotype from Illumina paired-end reads
01
tsv txt versions
SeroBA is a k-mer based pipeline to identify the Serotype from Illumina NGS reads for given references.
Severus is a somatic structural variation (SV) caller for long reads (both PacBio and ONT)
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log read_qual breakpoints_double read_alignments read_ids collapsed_dup loh all_vcf all_breakpoints_clusters_list all_breakpoints_clusters all_plots somatic_vcf somatic_breakpoints_clusters_list somatic_breakpoints_clusters somatic_plots versions
Calculate the relative coverage on the Gonosomes vs Autosomes from the output of samtools depth, with error bars.
010
json tsv versions
Demultiplex bgzip'd fastq files
012
sample_fastq metrics most_frequent_unmatched per_project_metrics per_sample_metrics sample_barcode_hop_metrics versions
Ligate multiple phased BCF/VCF files into a single whole chromosome file. Typically run to ligate multiple chunks of phased common variants.
012
merged_variants versions
Fast and accurate method for estimation of haplotypes (phasing)
Tool to phase common sites, typically SNP array data, or the first step of WES/WGS data.
0123401201201
phased_variant versions
Fast and accurate method for estimation of haplotypes (phasing)
Tool to phase rare variants onto a scaffold of common variants (output of phase_common / ligate). Require feature AVX2.
01234012301
phased_variant versions
Fast and accurate method for estimation of haplotypes (phasing)
Program to compute switch error rate and genotyping error rate given simulated or trio data.
01234012012
errors versions
Fast and accurate method for estimation of haplotypes (phasing)
The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using DNA reads generated by Oxford Nanopore flow cells as input. Please note Assembler is design to focus on speed, so assembly may be considered somewhat non-deterministic as final assembly may vary across executions. See https://github.com/chanzuckerberg/shasta/issues/296.
01
assembly gfa results versions
Determine Shigella serotype from Illumina or Oxford Nanopore reads
01
tsv hits versions
Determine Shigella serotype from assemblies or Illumina paired-end reads
01
tsv versions
build and deploy Shiny apps for interactively mining differential abundance data
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app versions
Provides Shiny applications for various array and NGS applications. Currently very RNA-seq centric, with plans for expansion.
Make plots for interpretation of differential abundance statistics
010123
volcanos_png volcanos_html versions
Provides Shiny applications for various array and NGS applications. Currently very RNA-seq centric, with plans for expansion.
Make exploratory plots for analysis of matrix data, including PCA, Boxplots and density plots
0123
boxplots_png boxplots_html densities_png densities_html pca2d_png pca2d_html pca3d_png pca3d_html mad_png mad_html dendro versions
Provides Shiny applications for various array and NGS applications. Currently very RNA-seq centric, with plans for expansion.
validate consistency of feature and sample annotations with matrices and contrasts
0120101
sample_meta feature_meta assays contrasts versions
Provides Shiny applications for various array and NGS applications. Currently very RNA-seq centric, with plans for expansion.
A windowed adaptive trimming tool for FASTQ files using quality
012
single_trimmed paired_trimmed singleton_trimmed log versions
Indexing of transcriptome for gene expression quantification using SimpleAF
012010101
index ref t2g versions
SimpleAF is a tool for quantification of gene expression from RNA-seq data
simpleaf is a program to simplify and customize the running and configuration of single-cell processing with alevin-fry.
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map quant versions
SimpleAF is a program to simplify and customize the running and configuration of single-cell processing with alevin-fry.
Serovar prediction of salmonella assemblies
01
tsv allele_fasta allele_json cgmlst_csv versions
Calculate pairwise distances and basic clustering from SKA sketches
012
distances cluster_list cluster_files dot versions
SKA (Split Kmer Analysis)
Create genome sketch using split k-mers
012
skf versions
SKA (Split Kmer Analysis)
Simple ANI calculation between reference and query genomes.
0101
dist versions
skani is a fast and robust tool for calculating ANI between metagenome assembled genomes and contigs.
Memory-efficient ANI database queries with skani.
0101
search versions
skani is a fast and robust tool for calculating ANI between metagenome assembled genomes and contigs.
Storing skani sketches/indices on disk.
01
sketch_dir sketch markers versions
skani is a fast and robust tool for calculating ANI between metagenome assembled genomes and contigs.
All-to-all ANI computation.
01
triangle versions
skani is a fast and robust tool for calculating ANI between metagenome assembled genomes and contigs.
Fast, efficient, lossless compression of FASTQ files.
01
sfq versions
tool to call the copy number of full-length SMN1, full-length SMN2, as well as SMN2ฮ7โ8 (SMN2 with a deletion of Exon7-8) from a whole-genome sequencing (WGS) BAM file.
012
smncopynumber run_metrics versions
smoove simplifies and speeds calling and genotyping SVs for short reads. It also improves specificity by removing many spurious alignment signals that are indicative of low-level noise and often contribute to spurious calls. Developed by Brent Pedersen.
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vcf versions
structural variant calling and genotyping with existing tools, but, smoothly
The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. This module runs a simple Snakemake pipeline based on input snakefile. Expect many limitations."
0101
outputs snakemake_dir versions
Create a SNAP index for reference genome
01234
index versions
Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
structural-variant calling with sniffles
012010100
vcf tbi snf versions
Core-SNP alignment from Snippy outputs
0120
aln full_aln tab vcf txt versions
Rapid bacterial SNP calling and core genome alignments
Rapid haploid variant calling
010
tab csv html vcf bed gff bam bai log aligned_fa consensus_fa consensus_subs_fa raw_vcf filt_vcf vcf_gz vcf_csi txt versions
Rapid bacterial SNP calling and core genome alignments
Genetic variant annotation and functional effect prediction toolbox
012
cache versions
SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes).
Genetic variant annotation and functional effect prediction toolbox
01001
vcf report summary_html genes_txt versions
SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes).
Annotate a VCF file with another VCF file
012012
vcf versions
SnpSift is a toolbox that allows you to filter and manipulate annotated files
The dbNSFP is an integrated database of functional predictions from multiple algorithms
012012
vcf versions
SnpSift is a toolbox that allows you to filter and manipulate annotated files
Splits/Joins VCF(s) file into chromosomes
01
out_vcfs versions
SnpSift is a toolbox that allows you to filter and manipulate annotated files
Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
01012
tsv html versions
Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
012010101
extract versions
Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
0120
html pairs_tsv samples_tsv versions
Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
Local sequence alignment tool for filtering, mapping and clustering.
010101
reads log index versions
The core algorithm is based on approximate seeds and allows for sensitive analysis of NGS reads. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data. SortMeRNA takes as input files of reads (fasta, fastq, fasta.gz, fastq.gz) and one or multiple rRNA database file(s), and sorts apart aligned and rejected reads into two files. Additional applications include clustering and taxonomy assignation available through QIIME v1.9.1. SortMeRNA works with Illumina, Ion Torrent and PacBio data, and can produce SAM and BLAST-like alignments.
Classifies and predicts the origin of metagenomic samples
010000
report versions
Compare many FracMinHash signatures generated by sourmash sketch.
01000
matrix labels csv versions
Compute and compare FracMinHash signatures for DNA and protein data sets.
Search a metagenome sourmash signature against one or many reference databases and return the minimum set of genomes that contain the k-mers in the metagenome.
0100000
result unassigned matches prefetch prefetchcsv versions
Compute and compare FracMinHash signatures for DNA data sets.
Create a database of sourmash signatures (a group of FracMinHash sketches) to be used as references.
010
signature_index versions
Compute and compare FracMinHash signatures for DNA data sets.
Create a signature (a group of FracMinHash sketches) of a sequence using sourmash
01
signatures versions
Compute and compare FracMinHash signatures for DNA and protein data sets.
Annotate list of metagenome members (based on sourmash signature matches) with taxonomic information.
010
result versions
Compute and compare FracMinHash signatures for DNA data sets.
Module to use the 10x Space Ranger pipeline to process 10x spatial transcriptomics data
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outs versions
Visium Spatial Gene Expression is a next-generation molecular profiling solution for classifying tissue based on total mRNA. Space Ranger is a set of analysis pipelines that process Visium Spatial Gene Expression data with brightfield and fluorescence microscope images. Space Ranger allows users to map the whole transcriptome in formalin fixed paraffin embedded (FFPE) and fresh frozen tissues to discover novel insights into normal development, disease pathology, and clinical translational research. Space Ranger provides pipelines for end to end analysis of Visium Spatial Gene Expression experiments.
Module to build a filtered GTF needed by the 10x Genomics Space Ranger tool. Uses the spaceranger mkgtf command.
0
gtf versions
Visium Spatial Gene Expression is a next-generation molecular profiling solution for classifying tissue based on total mRNA. Space Ranger is a set of analysis pipelines that process Visium Spatial Gene Expression data with brightfield and fluorescence microscope images. Space Ranger allows users to map the whole transcriptome in formalin fixed paraffin embedded (FFPE) and fresh frozen tissues to discover novel insights into normal development, disease pathology, and clinical translational research. Space Ranger provides pipelines for end to end analysis of Visium Spatial Gene Expression experiments.
Module to build the reference needed by the 10x Genomics Space Ranger tool. Uses the spaceranger mkref command.
000
reference versions
Visium Spatial Gene Expression is a next-generation molecular profiling solution for classifying tissue based on total mRNA. Space Ranger is a set of analysis pipelines that process Visium Spatial Gene Expression data with brightfield and fluorescence microscope images. Space Ranger allows users to map the whole transcriptome in formalin fixed paraffin embedded (FFPE) and fresh frozen tissues to discover novel insights into normal development, disease pathology, and clinical translational research. Space Ranger provides pipelines for end to end analysis of Visium Spatial Gene Expression experiments.
Assembles a small genome (bacterial, fungal, viral)
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scaffolds contigs transcripts gene_clusters gfa warnings log versions
Spotiflow, accurate and efficient spot detection with stereographic flow.
01
spots versions
Fast, efficient, lossless compression of FASTQ files.
012
spring versions
SPRING is a compression tool for Fastq files (containing up to 4.29 Billion reads)
Fast, efficient, lossless decompression of FASTQ files.
010
fastq versions
SPRING is a compression tool for Fastq files (containing up to 4.29 Billion reads)
Extract sequencing reads in FASTQ format from a given NCBI Sequence Read Archive (SRA).
0100
reads versions
SRA Toolkit and SDK from NCBI
Download sequencing data from the NCBI Sequence Read Archive (SRA).
0100
sra versions
SRA Toolkit and SDK from NCBI
Test for the presence of suitable NCBI settings or create them on the fly.
NO input
versions ncbi_settings
SRA Toolkit and SDK from NCBI
Short Read Sequence Typing for Bacterial Pathogens is a program designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes.
012
gene_results fullgene_results mlst_results pileup sorted_bam versions
Short Read Sequence Typing for Bacterial Pathogens
Serotype prediction of Streptococcus suis assemblies
01
tsv versions
Advanced sequence file format conversions
01000
cram gzi versions
Staden Package 'io_lib' (sometimes referred to as libstaden-read by distributions). This contains code for reading and writing a variety of Bioinformatics / DNA Sequence formats.
Predicts Staphylococcus aureus SCCmec type based on primers.
01
tsv versions
Align reads to a reference genome using STAR
010101000
log_final log_out log_progress versions bam bam_sorted bam_sorted_aligned bam_transcript bam_unsorted fastq tab spl_junc_tab read_per_gene_tab junction sam wig bedgraph
STAR is a software package for mapping DNA sequences against a large reference genome, such as the human genome.
Create index for STAR
0101
index versions
STAR is a software package for mapping DNA sequences against a large reference genome, such as the human genome.
Get the minimal allowed index version from STAR
NO input
index_version versions
STAR is a software package for mapping DNA sequences against a large reference genome, such as the human genome.
Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
01
results_xlsx summary_tsv detailed_summary_tsv resfinder_tsv plasmidfinder_tsv mlst_tsv settings_txt pointfinder_tsv versions
Scan genome contigs against the ResFinder and PointFinder databases. In order to use the PointFinder databases, you will have to add --pointfinder-organism ORGANISM to the ext.args options.
Cell and nuclear segmentation with star-convex shapes
01
mask versions
Serotype STEC samples from paired-end reads or assemblies
01
tsv versions
STITCH is an R program for reference panel free, read aware, low coverage sequencing genotype imputation. STITCH runs on a set of samples with sequencing reads in BAM format, as well as a list of positions to genotype, and outputs imputed genotypes in VCF format.
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input rdata plots vcf bgen versions
Annotates output files from ExpansionHunter with the pathologic implications of the repeat sizes.
0101
vcf versions
Tandem repeat genotyper for long reads
012010101
vcf tbi versions
Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation
0123400
vcf vcf_tbi genome_vcf genome_vcf_tbi versions
Strelka calls somatic and germline small variants from mapped sequencing reads
Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs
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vcf_indels vcf_indels_tbi vcf_snvs vcf_snvs_tbi versions
Strelka calls somatic and germline small variants from mapped sequencing reads
Merges the annotation gtf file and the stringtie output gtf files
00
gtf versions
Transcript assembly and quantification for RNA-Seq
Transcript assembly and quantification for RNA-Se
010
transcript_gtf abundance coverage_gtf ballgown versions
Transcript assembly and quantification for RNA-Seq
Count reads that map to genomic features
012
counts summary versions
featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations. It can be used to count both RNA-seq and genomic DNA-seq reads.
SummarizedExperiment container
010101
rds log versions
The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.
Converts a bedpe file to a VCF file (beta version)
01
vcf versions
Toolset for SV simulation, comparison and filtering
Filter a vcf file based on size and/or regions to ignore
0120000
vcf versions
Toolset for SV simulation, comparison and filtering
Compare or merge VCF files to generate a consensus or multi sample VCF files.
01000000
vcf versions
Toolset for SV simulation, comparison and filtering
Simulate an SV VCF file based on a reference genome
01010100
parameters vcf bed fasta insertions versions
Toolset for SV simulation, comparison and filtering
Report multiple stats over a VCF file
01000
stats versions
Toolset for SV simulation, comparison and filtering
SvABA is an efficient and accurate method for detecting SVs from short-read sequencing data using genome-wide local assembly with low memory and computing requirements
01234010101010101
sv indel germ_indel germ_sv som_indel som_sv unfiltered_sv unfiltered_indel unfiltered_germ_indel unfiltered_germ_sv unfiltered_som_indel unfiltered_som_sv raw_calls discordants log versions
SVbenchmark compares a set of โtestโ structural variants in VCF format to a known truth set (also in VCF format) and outputs estimates of sensitivity and specificity.
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fns fps distances log report versions
SVanalyzer: tools for the analysis of structural variation in genomes
Build a structural variant database
010
db versions
structural variant database software
The merge module merges structural variants within one or more vcf files.
0100
vcf tbi csi versions
structural variant database software
Query a structural variant database, using a vcf file as query
01000000
vcf versions
structural variant database software
Performs tests on BAF files
01234
metrics versions
Utilities for consolidating, filtering, resolving, and annotating structural variants.
Count the instances of each SVTYPE observed in each sample in a VCF.
01
counts versions
Utilities for consolidating, filtering, resolving, and annotating structural variants.
Convert an RdTest-formatted bed to the standard VCF format.
0120
vcf tbi versions
Utilities for consolidating, filtering, resolving, and annotating structural variants.
Convert SV calls to a standardized format.
0101
vcf versions
Utilities for consolidating, filtering, resolving, and annotating structural variants.
Converts VCFs containing structural variants to BED format
012
bed versions
Utilities for consolidating, filtering, resolving, and annotating structural variants.
Convert a VCF file to a BEDPE file.
01
bedpe versions
Tools for processing and analyzing structural variants
SVTyper performs breakpoint genotyping of structural variants (SVs) using whole genome sequencing data
01230101
json gt_vcf bam versions
Compute genotype of structural variants based on breakpoint depth
SVTyper-sso computes structural variant (SV) genotypes based on breakpoint depth on a SINGLE sample
012301
gt_vcf json versions
Bayesian genotyper for structural variants
A tool to standardize VCF files from structural variant callers
0123
vcf tbi versions
Sylph profile command for taxonoming profiling
010
profile_out versions
Sylph quickly enables querying of genomes against even low-coverage shotgun metagenomes to find nearest neighbour ANI.
Sketching/indexing sequencing reads
010
sketch_fastq_genome versions
Sylph quickly enables querying of genomes against even low-coverage shotgun metagenomes to find nearest neighbour ANI.
Incorporates taxonomy into sylph metagenomic classifier
010
taxprof_output versions
Integrating taxonomic information into the sylph metagenome profiler.
Compresses/decompresses files
01
output gzi versions
Bgzip compresses or decompresses files in a similar manner to, and compatible with, gzip.
create tabix index from a sorted bgzip tab-delimited genome file
01
tbi csi versions
Generic indexer for TAB-delimited genome position files.
Estimating poly(A)-tail lengths from basecalled fast5 files produced by Nanopore sequencing of RNA and DNA
01
csv_gz versions
Convert taxonids to taxon lineages
0120
tsv versions
A Cross-platform and Efficient NCBI Taxonomy Toolkit
Convert taxon names to TaxIds
0120
tsv versions
A Cross-platform and Efficient NCBI Taxonomy Toolkit
Standardise and merge two or more taxonomic profiles into a single table
010000
merged_profiles versions
TAXonomic Profile Aggregation and STAndardisation
Standardise the output of a wide range of taxonomic profilers
01000
standardised_profile versions
TAXonomic Profile Aggregation and STAndardisation
A tool to detect resistance and lineages of M. tuberculosis genomes
01
bam csv json txt vcf versions
Profiling tool for Mycobacterium tuberculosis to detect drug resistance and lineage from WGS data
Aligns sequences using T_COFFEE
01010120
alignment lib versions
A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.
Parallel implementation of the gzip algorithm.
Compares 2 alternative MSAs to evaluate them.
012
scores versions
A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence
Parallel implementation of the gzip algorithm.
Computes a consensus alignment using T_COFFEE
01010
alignment eval versions
A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.
Parallel implementation of the gzip algorithm.
Reformats the header of PDB files with t-coffee
01
formatted_pdb versions
A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.
Computes the irmsd score for a given alignment and the structures.
01012
irmsd versions
A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence
Parallel implementation of the gzip algorithm.
Aligns sequences using the regressive algorithm as implemented in the T_COFFEE package
01010120
alignment versions
A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.
Parallel implementation of the gzip algorithm.
Reformats files with t-coffee
01
formatted_file versions
A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.
Compute the TCS score for a MSA or for a MSA plus a library file. Outputs the tcs as it is and a csv with just the total TCS score.
0101
tcs scores versions
A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence
Parallel implementation of the gzip algorithm.
Parses a Thermo RAW file containing mass spectra to an open file format
01
spectra versions
Domain-level classification of contigs to bacterial, archaeal, eukaryotic, or organelle
01
classifications log fasta versions
Deep-learning-based approach for identification of eukaryotic sequences in the metagenomic data powered by PyTorch.
Computes the coverage of different regions from the bam file.
0101
cov wig versions
TIDDIT - structural variant calling.
Identify chromosomal rearrangements.
0120101
vcf ploidy versions
Search for structural variants.
tidk explore attempts to find the simple telomeric repeat unit in the genome provided.
It will report this repeat in its canonical form (e.g. TTAGG -> AACCT).
01
explore_tsv top_sequence versions
tidk is a toolkit to identify and visualise telomeric repeats in genomes
Searches a genome for a telomere string such as TTAGGG
010
tsv bedgraph versions
tidk is a toolkit to identify and visualise telomeric repeats in genomes
Create fasta consensus with TOPAS toolkit with options to penalize substitutions for typical DNA damage present in ancient DNA
010101010
fasta vcf ccf log versions
This toolkit allows the efficient manipulation of sequence data in various ways. It is organized into modules: The FASTA processing modules, the FASTQ processing modules, the GFF processing modules and the VCF processing modules.
A post sequencing QC tool for Oxford Nanopore sequencers
01
report_data report_html plots_html plotly_js versions
TransDecoder identifies candidate coding regions within transcript sequences. it is used to build gff file.
01
pep gff3 cds dat folder versions
TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.
TransDecoder identifies candidate coding regions within transcript sequences. It is used to build gff file. You can use this module after transdecoder_longorf
010
pep gff3 cds bed versions
TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.
Tandem repeat genotyping from PacBio HiFi data
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vcf bam versions
Tandem repeat genotyping and visualization from PacBio HiFi data
Merge TRGT VCFs from multiple samples
0120101
vcf versions
Tandem repeat genotyping and visualization from PacBio HiFi data
Trim FastQ files using Trim Galore!
01
reads log unpaired html zip versions
Performs quality and adapter trimming on paired end and single end reads
01
trimmed_reads unpaired_reads trim_log out_log summary versions
Assembles a de novo transcriptome from RNAseq reads
01
transcript_fasta log versions
Detection of tRNA sequences using covariance models
01
tsv log stats fasta gff bed versions
Given baseline and comparison sets of variants, calculate the recall/precision/f-measure
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fn_vcf fn_tbi fp_vcf fp_tbi tp_base_vcf tp_base_tbi tp_comp_vcf tp_comp_tbi summary versions
Structural variant comparison tool for VCFs
Over multiple vcfs, calculate their intersection/consistency.
01
consistency versions
Structural variant comparison tool for VCFs
Normalization of SVs into disjointed genomic regions
01
vcf versions
Structural variant comparison tool for VCFs
Subsample a long-read sequencing fastq file for multiple assemblies
01
subreads versions
Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes
Transcript Selector for BRAKER TSEBRA combines gene predictions by selecting transcripts based on their extrisic evidence support
01000
tsebra_gtf tsebra_scores versions
Import transcript-level abundances and estimated counts for gene-level analysis packages
01010
tpm_gene counts_gene counts_gene_length_scaled counts_gene_scaled lengths_gene tpm_transcript counts_transcript lengths_transcript versions
Transcript Quantification Import with Automatic Metadata
Remove lines from bed file that refer to off-chromosome locations.
010
bedgraph versions
Remove lines from bed file that refer to off-chromosome locations.
Convert a bedGraph file to bigWig format.
010
bigwig versions
Convert a bedGraph file to bigWig format.
Convert file from bed to bigBed format
0100
bigbed versions
Convert file from bed to bigBed format
compute average score of bigwig over bed file
010
tab versions
Compute average score of big wig over each bed, which may have introns.
compute average score of bigwig over bed file
01
genepred refflat versions
Convert GTF files to GenePred format
convert between genome builds
010
lifted unlifted versions
Move annotations from one assembly to another
Convert ascii format wig file to binary big wig format
010
bw versions
Convert ascii format wig file (in fixedStep, variableStep or bedGraph format) to binary big wig format
Ultraplex is an all-in-one software package for processing and demultiplexing fastq files.
010
fastq no_match_fastq report versions
Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read.
0120
bam fastq log versions
Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read.
0120
bam log tsv_edit_distance tsv_per_umi tsv_umi_per_position versions
UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes
Extracts UMI barcode from a read and add it to the read name, leaving any sample barcode in place
01
reads log versions
UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes
Group reads based on their UMI and mapping coordinates
01200
log bam tsv versions
UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes
Make the output from umi_tools dedup or group compatible with RSEM
012
bam log versions
UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes
Assembles bacterial genomes
012
scaffolds gfa log versions
Module to run UniverSC an open-source pipeline to demultiplex and process single-cell RNA-Seq data
010
outs versions
Unzip ZIP archive files
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files versions
p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip, see www.7-zip.org) for Unix.
Simple software to call UPD regions from germline exome/wgs trios.
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bed versions
The Java port of the VarDict variant caller
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vcf versions
Runs a differential expression analysis with dream() from variancePartition R package
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results model versions
Differential expression for repeated measures
Filtering, downsampling and profiling alignments in BAM/CRAM formats
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bam versions
Call variants for a given scenario specified with the varlociraptor calling grammar, preprocessed by varlociraptor preprocessing
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bcf_gz vcf_gz bcf vcf versions
Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control.
In order to judge about candidate indel and structural variants, Varlociraptor needs to know about certain properties of the underlying sequencing experiment in combination with the used read aligner.
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alignment_properties_json versions
Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control.
Obtains per-sample observations for the actual calling process with varlociraptor calls
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bcf_gz vcf_gz bcf vcf versions
Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control.
Convert VCF with structural variations to CytoSure format
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cgh versions
If multiple alleles are specified in a single record, break the record into several lines preserving allele-specific INFO fields
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vcf versions
Command-line tools for manipulating VCF files
Command line tools for parsing and manipulating VCF files.
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vcf versions
Command line tools for parsing and manipulating VCF files.
Generates a VCF stream where AC and NS have been generated for each record using sample genotypes.
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vcf versions
Command-line tools for manipulating VCF files
List unique genotypes. Like GNU uniq, but for VCF records. Remove records which have the same position, ref, and alt as the previous record.
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vcf versions
Command-line tools for manipulating VCF files
A set of tools written in Perl and C++ for working with VCF files
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vcf bcf frq frq_count idepth ldepth ldepth_mean gdepth hap_ld geno_ld geno_chisq list_hap_ld list_geno_ld interchrom_hap_ld interchrom_geno_ld tstv tstv_summary tstv_count tstv_qual filter_summary sites_pi windowed_pi weir_fst heterozygosity hwe tajima_d freq_burden lroh relatedness relatedness2 lqual missing_individual missing_site snp_density kept_sites removed_sites singeltons indel_hist hapcount mendel format info genotypes_matrix genotypes_matrix_individual genotypes_matrix_position impute_hap impute_hap_legend impute_hap_indv ldhat_sites ldhat_locs beagle_gl beagle_pl ped map_ tped tfam diff_sites_in_files diff_indv_in_files diff_sites diff_indv diff_discd_matrix diff_switch_error versions
Velocyto is a library for the analysis of RNA velocity. velocyto.py CLI use
Path(resolve_path=True) and breaks the nextflow logic of symbolic links.
If in the work dir velocyto find a file named EXACTLY cellsorted_[ORIGINAL_BAM_NAME]
it will skip the samtools sort step.
Cellsorted bam file should be cell sorted with:
samtools sort -t CB -O BAM -o cellsorted_input.bam input.bamSee module test for an example with the SAMTOOLS_SORT nf-core module. Config example to cellsort input bam using SAMTOOLS_SORT:
withName: SAMTOOLS_SORT {
ext.prefix = { "cellsorted_${bam.baseName}" }
ext.args = '-t CB -O BAM'
}Optional mask must be passed with ext.args and option --mask
This is why I need to stage in the work dir 2 bam files (cellsorted and original).
See also velocyto tutorial
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loom versions
Detecting and estimating inter-sample DNA contamination became a crucial quality assessment step to ensure high quality sequence reads and reliable downstream analysis.
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log selfsm depthsm selfrg depthrg bestsm bestrg versions
verifyBamID is a software that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of two samples.
Detecting and estimating inter-sample DNA contamination became a crucial quality assessment step to ensure high quality sequence reads and reliable downstream analysis.
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log ud bed mu self_sm ancestry versions
A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
Constructs a graph from a reference and variant calls or a multiple sequence alignment file
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graph versions
Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods.
Deconstruct snarls present in a variation graph in GFA format to variants in VCF format
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vcf versions
Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods.
write your description here
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xg vg_index versions
Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods.
calculate secondary structures of two RNAs with dimerization
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rnacofold_csv rnacofold_ps versions
calculate secondary structures of two RNAs with dimerization
The program works much like RNAfold, but allows one to specify two RNA sequences which are then allowed to form a dimer structure. RNA sequences are read from stdin in the usual format, i.e. each line of input corresponds to one sequence, except for lines starting with > which contain the name of the next sequence. To compute the hybrid structure of two molecules, the two sequences must be concatenated using the & character as separator. RNAcofold can compute minimum free energy (mfe) structures, as well as partition function (pf) and base pairing probability matrix (using the -p switch) Since dimer formation is concentration dependent, RNAcofold can be used to compute equilibrium concentrations for all five monomer and (homo/hetero)-dimer species, given input concentrations for the monomers. Output consists of the mfe structure in bracket notation as well as PostScript structure plots and โdot plotโ files containing the pair probabilities, see the RNAfold man page for details. In the dot plots a cross marks the chain break between the two concatenated sequences. The program will continue to read new sequences until a line consisting of the single character @ or an end of file condition is encountered.
Predict RNA secondary structure using the ViennaRNA RNAfold tools. Calculate minimum free energy secondary structures and partition function of RNAs.
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rnafold_txt rnafold_ps versions
Calculate minimum free energy secondary structures and partition function of RNAs
The program reads RNA sequences, calculates their minimum free energy (mfe) structure and prints the mfe structure in bracket notation and its free energy. If not specified differently using commandline arguments, input is accepted from stdin or read from an input file, and output printed to stdout. If the -p option was given it also computes the partition function (pf) and base pairing probability matrix, and prints the free energy of the thermodynamic ensemble, the frequency of the mfe structure in the ensemble, and the ensemble diversity to stdout.
calculate locally stable secondary structures of RNAs
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rnalfold_txt versions
calculate locally stable secondary structures of RNAs
Compute locally stable RNA secondary structure with a maximal base pair span. For a sequence of length n and a base pair span of L the algorithm uses only O(n+LL) memory and O(nL*L) CPU time. Thus it is practical to โscanโ very large genomes for short RNA structures. Output consists of a list of secondary structure components of size <= L, one entry per line. Each output line contains the predicted local structure its energy in kcal/mol and the starting position of the local structure.
Use vireo to perform donor deconvolution for multiplexed scRNA-seq data
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summary donor_ids prob_singlets prob_doublets versions
Extracting sequences that were unbinnned by vRhyme into a FASTA file
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unbinned_sequences versions
vRhyme functions by utilizing coverage variance comparisons and supervised machine learning classification of sequence features to construct viral metagenome-assembled genomes (vMAGs).
Linking bins output by vRhyme to create one sequences per bin
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linked_bins versions
vRhyme functions by utilizing coverage variance comparisons and supervised machine learning classification of sequence features to construct viral metagenome-assembled genomes (vMAGs).
Binning virus genomes from metagenomes
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bins membership summary versions
vRhyme functions by utilizing coverage variance comparisons and supervised machine learning classification of sequence features to construct viral metagenome-assembled genomes (vMAGs).
Cluster sequences using a single-pass, greedy centroid-based clustering algorithm.
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aln biom mothur otu bam out blast uc centroids clusters profile msa versions
VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)
Merge strictly identical sequences contained in filename. Identical sequences are defined as having the same length and the same string of nucleotides (case insensitive, T and U are considered the same).
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fasta clustering log versions
A versatile open source tool for metagenomics (USEARCH alternative)
Performs quality filtering and / or conversion of a FASTQ file to FASTA format.
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fasta log versions
VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)
Taxonomic classification using the sintax algorithm.
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tsv versions
VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)
Sort fasta entries by decreasing abundance (--sortbysize) or sequence length (--sortbylength).
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fasta versions
VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)
Compare target sequences to fasta-formatted query sequences using global pairwise alignment.
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aln biom lca mothur otu sam tsv txt uc versions
VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)
decomposes multiallelic variants into biallelic in a VCF file.
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vcf versions
A tool set for short variant discovery in genetic sequence data
Decomposes biallelic block substitutions into its constituent SNPs.
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vcf versions
A tool set for short variant discovery in genetic sequence data
normalizes variants in a VCF file
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vcf fai versions
A tool set for short variant discovery in genetic sequence data
a pangenome-scale aligner
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paf versions
The wham suite consists of two programs, wham and whamg. wham, the original tool, is a very sensitive method with a high false discovery rate. The second program, whamg, is more accurate and better suited for general structural variant (SV) discovery.
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vcf tbi graph versions
Masks out highly repetitive DNA sequences with low complexity in a genome
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converted versions
A program to mask highly repetitive and low complexity DNA sequences within a genome.
A program to generate frequency counts of repetitive units.
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counts versions
A program to mask highly repetitive and low complexity DNA sequences within a genome.
A program to take a counts file and creates a file of genomic co-ordinates to be masked.
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intervals versions
A program to mask highly repetitive and low complexity DNA sequences within a genome.
A tool of the wipertools suite that merges FASTQ chunks produced by wipertools_fastqscatter
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gathered_fastq versions
A tool of the wipertools suite that merges FASTQ chunks produced by wipertools_fastqscatter.
A tool of the wipertools suite that splits FASTQ files into chunks
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fastq_chunks versions
A tool of the wipertools suite that splits FASTQ files into chunks.
A tool of the wipertools suite that fixes or wipes out uncompliant reads from FASTQ files
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wiped_fastq report versions
A tool of the wipertools suite that that fixes or wipes out uncompliant reads from FASTQ files.
A tool of the wipertools suite that merges wiping reports generated by wipertools_fastqwiper
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gathered_report versions
A tool of the wipertools suite that merges wiping reports generated by wipertools_fastqwiper.
Convert and filter aligned reads to .npz
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npz versions
WIthin-SamplE COpy Number aberration DetectOR, including sex chromosomes
Returns the gender of a .npz resulting from convert, based on a Gaussian mixture model trained during the newref phase
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gender versions
WIthin-SamplE COpy Number aberration DetectOR, including sex chromosomes
Create a new reference using healthy reference samples
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npz versions
WIthin-SamplE COpy Number aberration DetectOR, including sex chromosomes
Find copy number aberrations
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aberrations_bed bins_bed segments_bed chr_statistics chr_plots genome_plot versions
WIthin-SamplE COpy Number aberration DetectOR, including sex chromosomes
A large variant benchmarking tool analogous to hap.py for small variants.
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report bench_vcf bench_vcf_tbi versions
The xeniumranger import-segmentation module allows you to specify 2D nuclei and/or cell segmentation results for assigning transcripts to cells and recalculate all Xenium Onboard Analysis (XOA) outputs that depend on segmentation. Segmentation results can be generated by community-developed tools or prior Xenium segmentation result.
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outs versions
Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells.
The xeniumranger relabel module allows you to change the gene labels applied to decoded transcripts.
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outs versions
Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells.
The xeniumranger rename module allows you to change the sample region_name and cassette_name throughout all the Xenium Onboard Analysis output files that contain this information.
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outs versions
Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells.
The xeniumranger resegment module allows you to generate a new segmentation of the morphology image space by rerunning the Xenium Onboard Analysis (XOA) segmentation algorithms with modified parameters.
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outs versions
Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells.
Compresses files with xz.
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archive versions
xz is a general-purpose data compression tool with command line syntax similar to gzip and bzip2.
Decompresses files with xz.
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file versions
xz is a general-purpose data compression tool with command line syntax similar to gzip and bzip2.
Performs assembly scaffolding using YaHS
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scaffolds_fasta scaffolds_agp binary versions
Align reads to a reference genome using YARA
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bam bai versions
Yara is an exact tool for aligning DNA sequencing reads to reference genomes.
Compress file lists to produce ZIP archive files
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zipped_archive versions
p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip, see www.7-zip.org) for Unix.
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