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.

  • binning 15
  • bam 10
  • contigs 9
  • bins 9
  • bed 8
  • cooler 8
  • fasta 6
  • vcf 6
  • genomics 6
  • metagenomics 6
  • sort 6
  • merge 6
  • mags 6
  • assembly 5
  • coverage 5
  • fragment 5
  • contamination 4
  • quality 4
  • bcftools 4
  • table 4
  • depth 4
  • checkm 4
  • metagenome 4
  • completeness 4
  • mag 4
  • bin 4
  • genome 3
  • index 3
  • database 3
  • imputation 3
  • ncbi 3
  • de novo 3
  • de novo assembly 3
  • cut 3
  • public datasets 3
  • hic 3
  • entrez 3
  • vrhyme 3
  • combine 3
  • cut up 3
  • cool 3
  • das tool 3
  • das_tool 3
  • reference 2
  • alignment 2
  • gatk4 2
  • cram 2
  • variants 2
  • cnv 2
  • split 2
  • gfa 2
  • gvcf 2
  • reporting 2
  • prediction 2
  • isolates 2
  • microbes 2
  • recombination 2
  • single cells 2
  • genome bins 2
  • sam 1
  • annotation 1
  • gff 1
  • gtf 1
  • variant 1
  • pacbio 1
  • convert 1
  • copy number 1
  • bedtools 1
  • phylogeny 1
  • variation graph 1
  • kmer 1
  • antimicrobial resistance 1
  • phage 1
  • metrics 1
  • amr 1
  • pangenome graph 1
  • cluster 1
  • expression 1
  • genotype 1
  • virus 1
  • bcf 1
  • low-coverage 1
  • transcript 1
  • peaks 1
  • phasing 1
  • glimpse 1
  • example 1
  • gene 1
  • ucsc 1
  • differential 1
  • bedGraph 1
  • prokaryote 1
  • multiple sequence alignment 1
  • text 1
  • query 1
  • counts 1
  • interval 1
  • merging 1
  • compare 1
  • bigwig 1
  • concatenate 1
  • npz 1
  • wastewater 1
  • transcripts 1
  • fam 1
  • bim 1
  • wig 1
  • png 1
  • comparisons 1
  • bracken 1
  • dump 1
  • kraken 1
  • concordance 1
  • krakentools 1
  • scaffolding 1
  • tbi 1
  • deconvolution 1
  • cvnkit 1
  • merge mate pairs 1
  • reads merging 1
  • evidence 1
  • estimation 1
  • deseq2 1
  • rna-seq 1
  • metadata 1
  • copy number variation 1
  • yahs 1
  • extractunbinned 1
  • linkbins 1
  • tags 1
  • impute-info 1
  • selector 1
  • setgt 1
  • qa 1
  • quality assurnce 1
  • postprocessing 1
  • combining 1
  • unionBedGraphs 1
  • preprocessintervals 1
  • mcool 1
  • genomic bins 1
  • makebins 1
  • enzyme 1
  • digest 1
  • cload 1
  • cooler/balance 1
  • subcontigs 1
  • nucleotide composition 1
  • concoct 1
  • short variant discovery 1
  • combinegvcfs 1
  • bootstrapping 1
  • antitarget 1
  • csi 1
  • assembly-binning 1
  • duplicate marking 1
  • metagenome-assembled genomes 1
  • maxbin2 1
  • overlapped bed 1
  • paragraph 1
  • pbbam 1
  • pbmerge 1
  • graph stats 1
  • squeeze 1
  • odgi 1
  • combine graphs 1
  • fastq 0
  • structural variants 0
  • variant calling 0
  • align 0
  • filter 0
  • bacteria 0
  • map 0
  • statistics 0
  • qc 0
  • quality control 0
  • classify 0
  • download 0
  • nanopore 0
  • taxonomic profiling 0
  • MSA 0
  • k-mer 0
  • somatic 0
  • taxonomy 0
  • sentieon 0
  • classification 0
  • conversion 0
  • count 0
  • single-cell 0
  • clustering 0
  • VCF 0
  • proteomics 0
  • ancient DNA 0
  • graph 0
  • trimming 0
  • isoseq 0
  • build 0
  • sv 0
  • bisulfite 0
  • consensus 0
  • illumina 0
  • picard 0
  • rnaseq 0
  • databases 0
  • wgs 0
  • methylseq 0
  • bisulphite 0
  • methylation 0
  • bqsr 0
  • protein 0
  • cna 0
  • compression 0
  • indexing 0
  • QC 0
  • 5mC 0
  • mapping 0
  • long-read 0
  • imaging 0
  • stats 0
  • serotype 0
  • tsv 0
  • visualisation 0
  • demultiplex 0
  • sequences 0
  • scWGBS 0
  • WGBS 0
  • DNA methylation 0
  • haplotype 0
  • markduplicates 0
  • pairs 0
  • base quality score recalibration 0
  • searching 0
  • protein sequence 0
  • histogram 0
  • openms 0
  • structure 0
  • neural network 0
  • plot 0
  • matrix 0
  • aDNA 0
  • repeat 0
  • LAST 0
  • palaeogenomics 0
  • mmseqs2 0
  • machine learning 0
  • archaeogenomics 0
  • mappability 0
  • damage 0
  • filtering 0
  • iCLIP 0
  • annotate 0
  • db 0
  • validation 0
  • samtools 0
  • bwa 0
  • biscuit 0
  • aligner 0
  • bisulfite sequencing 0
  • transcriptome 0
  • decompression 0
  • gff3 0
  • segmentation 0
  • mkref 0
  • dedup 0
  • population genetics 0
  • msa 0
  • kraken2 0
  • blast 0
  • bismark 0
  • hmmsearch 0
  • evaluation 0
  • genotyping 0
  • spatial 0
  • newick 0
  • long reads 0
  • seqkit 0
  • complexity 0
  • sequence 0
  • umi 0
  • germline 0
  • pangenome 0
  • plasmid 0
  • demultiplexing 0
  • scRNA-seq 0
  • splicing 0
  • kmers 0
  • low frequency variant calling 0
  • mirna 0
  • vsearch 0
  • hmmer 0
  • cnvkit 0
  • short-read 0
  • report 0
  • single 0
  • NCBI 0
  • antimicrobial peptides 0
  • gzip 0
  • snp 0
  • duplicates 0
  • deduplication 0
  • mitochondria 0
  • json 0
  • tumor-only 0
  • feature 0
  • antimicrobial resistance genes 0
  • gridss 0
  • MAF 0
  • amps 0
  • visualization 0
  • detection 0
  • 3-letter genome 0
  • single cell 0
  • arg 0
  • summary 0
  • kallisto 0
  • call 0
  • clipping 0
  • wxs 0
  • mem 0
  • idXML 0
  • mutect2 0
  • view 0
  • antibiotic resistance 0
  • extract 0
  • indels 0
  • mpileup 0
  • deamination 0
  • adapters 0
  • benchmark 0
  • microbiome 0
  • csv 0
  • profiling 0
  • svtk 0
  • ptr 0
  • riboseq 0
  • coptr 0
  • tabular 0
  • diversity 0
  • sourmash 0
  • taxonomic classification 0
  • enrichment 0
  • genome assembler 0
  • bcl2fastq 0
  • fgbio 0
  • snps 0
  • read depth 0
  • CLIP 0
  • gsea 0
  • circrna 0
  • haplotypecaller 0
  • bedgraph 0
  • genmod 0
  • SV 0
  • ranking 0
  • compress 0
  • peak-calling 0
  • diamond 0
  • deep learning 0
  • miscoding lesions 0
  • structural 0
  • palaeogenetics 0
  • phylogenetic placement 0
  • ganon 0
  • interval_list 0
  • archaeogenetics 0
  • profile 0
  • STR 0
  • paf 0
  • cat 0
  • chunk 0
  • ATAC-seq 0
  • FASTQ 0
  • fastx 0
  • sample 0
  • sequencing 0
  • DNA sequencing 0
  • umitools 0
  • targeted sequencing 0
  • hybrid capture sequencing 0
  • copy number alteration calling 0
  • normalization 0
  • sketch 0
  • add 0
  • ont 0
  • resistance 0
  • union 0
  • ampir 0
  • xeniumranger 0
  • ancestry 0
  • pypgx 0
  • isomir 0
  • microarray 0
  • parsing 0
  • retrotransposon 0
  • fungi 0
  • malt 0
  • telomere 0
  • redundancy 0
  • BGC 0
  • biosynthetic gene cluster 0
  • propr 0
  • logratio 0
  • family 0
  • bgzip 0
  • ccs 0
  • hmmcopy 0
  • DNA sequence 0
  • reference-free 0
  • microsatellite 0
  • reads 0
  • quantification 0
  • ngscheckmate 0
  • containment 0
  • matching 0
  • HiFi 0
  • preprocessing 0
  • happy 0
  • reports 0
  • notebook 0
  • bedpe 0
  • gatk4spark 0
  • mzml 0
  • somatic variants 0
  • ligate 0
  • amplicon sequences 0
  • mtDNA 0
  • windowmasker 0
  • pseudoalignment 0
  • krona chart 0
  • variant_calling 0
  • mapper 0
  • typing 0
  • guide tree 0
  • covid 0
  • organelle 0
  • transcriptomics 0
  • repeat expansion 0
  • fcs-gx 0
  • chimeras 0
  • PacBio 0
  • fingerprint 0
  • PCA 0
  • miRNA 0
  • ambient RNA removal 0
  • HMM 0
  • amplicon sequencing 0
  • rna_structure 0
  • RNA 0
  • genotype-based deconvoltion 0
  • cfDNA 0
  • popscle 0
  • dna 0
  • transposons 0
  • krona 0
  • bacterial 0
  • untar 0
  • archiving 0
  • plink2 0
  • rsem 0
  • genome assembly 0
  • polishing 0
  • indel 0
  • mlst 0
  • spark 0
  • prokka 0
  • dictionary 0
  • duplication 0
  • insert 0
  • score 0
  • replace 0
  • pairsam 0
  • structural_variants 0
  • pan-genome 0
  • lineage 0
  • SNP 0
  • benchmarking 0
  • unzip 0
  • survivor 0
  • uncompress 0
  • fastk 0
  • pangolin 0
  • html 0
  • long_read 0
  • panel 0
  • minimap2 0
  • uLTRA 0
  • tabix 0
  • spaceranger 0
  • subsample 0
  • UMI 0
  • informative sites 0
  • kinship 0
  • identity 0
  • relatedness 0
  • lossless 0
  • small indels 0
  • observations 0
  • shapeit 0
  • scores 0
  • zip 0
  • arriba 0
  • rna 0
  • adapter trimming 0
  • angsd 0
  • ataqv 0
  • aln 0
  • abundance 0
  • bwameth 0
  • CRISPR 0
  • hi-c 0
  • pileup 0
  • DRAMP 0
  • bamtools 0
  • nucleotide 0
  • quality trimming 0
  • fusion 0
  • amplify 0
  • fai 0
  • intervals 0
  • converter 0
  • virulence 0
  • genome mining 0
  • chromosome 0
  • roh 0
  • prokaryotes 0
  • eukaryotes 0
  • complement 0
  • RNA-seq 0
  • remove 0
  • macrel 0
  • image 0
  • mcmicro 0
  • prefetch 0
  • highly_multiplexed_imaging 0
  • atac-seq 0
  • image_analysis 0
  • cellranger 0
  • bakta 0
  • genomes 0
  • deeparg 0
  • C to T 0
  • chip-seq 0
  • neubi 0
  • gene expression 0
  • mkfastq 0
  • host 0
  • clean 0
  • checkv 0
  • MaltExtract 0
  • phase 0
  • long terminal repeat 0
  • retrotransposons 0
  • pair 0
  • variation 0
  • pharokka 0
  • interactive 0
  • differential expression 0
  • function 0
  • HOPS 0
  • primer 0
  • authentication 0
  • orthology 0
  • parallelized 0
  • checksum 0
  • tree 0
  • transcriptomic 0
  • mudskipper 0
  • minhash 0
  • mash 0
  • edit distance 0
  • vdj 0
  • xz 0
  • archive 0
  • COBS 0
  • k-mer index 0
  • bloom filter 0
  • lofreq 0
  • gene set analysis 0
  • serogroup 0
  • barcode 0
  • krakenuniq 0
  • awk 0
  • hlala_typing 0
  • hidden Markov model 0
  • Read depth 0
  • mask 0
  • leviosam2 0
  • lift 0
  • mapcounter 0
  • metamaps 0
  • hla_typing 0
  • ichorcna 0
  • taxon name 0
  • hlala 0
  • hla 0
  • genetics 0
  • functional analysis 0
  • taxids 0
  • regression 0
  • interactions 0
  • zlib 0
  • proteome 0
  • long terminal retrotransposon 0
  • polyA_tail 0
  • kma 0
  • screen 0
  • khmer 0
  • bustools 0
  • salmon 0
  • BAM 0
  • blastn 0
  • gene set 0
  • orf 0
  • immunoprofiling 0
  • refine 0
  • maximum likelihood 0
  • gstama 0
  • tama 0
  • iphop 0
  • trancriptome 0
  • instrain 0
  • windows 0
  • spatial_omics 0
  • megan 0
  • Duplication purging 0
  • small genome 0
  • de novo assembler 0
  • junctions 0
  • svdb 0
  • runs_of_homozygosity 0
  • polish 0
  • scaffold 0
  • contig 0
  • standardization 0
  • duplicate 0
  • taxonomic profile 0
  • graft 0
  • standardise 0
  • standardisation 0
  • otu tables 0
  • purge duplications 0
  • taxon tables 0
  • trim 0
  • library 0
  • preseq 0
  • adapter 0
  • demultiplexed reads 0
  • rtgtools 0
  • signature 0
  • import 0
  • effect prediction 0
  • ancient dna 0
  • sequenzautils 0
  • switch 0
  • transformation 0
  • rename 0
  • shigella 0
  • seqtk 0
  • salmonella 0
  • varcal 0
  • fusions 0
  • soft-clipped clusters 0
  • snpeff 0
  • xenograft 0
  • snpsift 0
  • cancer genomics 0
  • fixmate 0
  • join 0
  • dict 0
  • collate 0
  • bam2fq 0
  • FracMinHash sketch 0
  • aggregate 0
  • artic 0
  • intersection 0
  • cnvnator 0
  • NRPS 0
  • msisensor-pro 0
  • micro-satellite-scan 0
  • tumor 0
  • proportionality 0
  • msi 0
  • instability 0
  • MSI 0
  • homoploymer 0
  • ampgram 0
  • nucleotides 0
  • removal 0
  • multiallelic 0
  • small variants 0
  • rgfa 0
  • spatial_transcriptomics 0
  • resolve_bioscience 0
  • tnhaplotyper2 0
  • profiles 0
  • secondary metabolites 0
  • reformatting 0
  • GC content 0
  • mitochondrion 0
  • registration 0
  • simulate 0
  • ped 0
  • RNA-Seq 0
  • variant pruning 0
  • bfiles 0
  • distance 0
  • vcflib 0
  • vg 0
  • concat 0
  • read-group 0
  • intersect 0
  • nextclade 0
  • GPU-accelerated 0
  • normalize 0
  • norm 0
  • scatter 0
  • reheader 0
  • antismash 0
  • SimpleAF 0
  • antibiotics 0
  • graph layout 0
  • RiPP 0
  • image_processing 0
  • comparison 0
  • Streptococcus pneumoniae 0
  • amptransformer 0
  • sequence analysis 0
  • Pharmacogenetics 0
  • microbial 0
  • frame-shift correction 0
  • bayesian 0
  • long-read sequencing 0
  • CNV 0
  • pharmacogenetics 0
  • calling 0
  • short reads 0
  • doublets 0
  • gwas 0
  • realignment 0
  • unaligned 0
  • ome-tif 0
  • gatk 0
  • joint genotyping 0
  • eCLIP 0
  • repeats 0
  • panelofnormals 0
  • MCMICRO 0
  • mirdeep2 0
  • RNA sequencing 0
  • smrnaseq 0
  • filtermutectcalls 0
  • interval list 0
  • allele-specific 0
  • anndata 0
  • UMIs 0
  • parse 0
  • fasterq-dump 0
  • sra-tools 0
  • eigenstrat 0
  • validate 0
  • samplesheet 0
  • format 0
  • eido 0
  • blastp 0
  • mRNA 0
  • structural-variant calling 0
  • metagenomes 0
  • heatmap 0
  • random forest 0
  • regions 0
  • settings 0
  • nanostring 0
  • duplex 0
  • repeat_expansions 0
  • fetch 0
  • GEO 0
  • metagenomic 0
  • identifier 0
  • gene labels 0
  • expansionhunterdenovo 0
  • nacho 0
  • screening 0
  • cleaning 0
  • tab 0
  • trgt 0
  • correction 0
  • emboss 0
  • corrupted 0
  • dereplicate 0
  • cnv calling 0
  • genomad 0
  • baf 0
  • ChIP-seq 0
  • gem 0
  • allele 0
  • sage 0
  • vcflib/vcffixup 0
  • umicollapse 0
  • trimfq 0
  • nanopore sequencing 0
  • scRNA-Seq 0
  • morphology 0
  • resegment 0
  • AC/NS/AF 0
  • files 0
  • relabel 0
  • hostile 0
  • Pacbio 0
  • adapterremoval 0
  • cell segmentation 0
  • upd 0
  • uniparental 0
  • disomy 0
  • snv 0
  • downsample 0
  • downsample bam 0
  • antimicrobial reistance 0
  • mkarv 0
  • decontamination 0
  • atlas 0
  • contiguate 0
  • scanpy 0
  • Mycobacterium tuberculosis 0
  • chromosomal rearrangements 0
  • eucaryotes 0
  • extension 0
  • coding 0
  • cds 0
  • transcroder 0
  • sequencing adapters 0
  • bedgraphtobigwig 0
  • rna velocity 0
  • bigbed 0
  • bedtobigbed 0
  • genepred 0
  • refflat 0
  • gtftogenepred 0
  • ucsc/liftover 0
  • cobra 0
  • metagenome assembler 0
  • vcf2db 0
  • human removal 0
  • subsample bam 0
  • lua 0
  • gemini 0
  • logFC 0
  • pangenome-scale 0
  • all versus all 0
  • mashmap 0
  • wavefront 0
  • whamg 0
  • wham 0
  • bwameme 0
  • HLA 0
  • copy-number 0
  • grabix 0
  • bwamem2 0
  • copy number analysis 0
  • subsetting 0
  • pile up 0
  • barcodes 0
  • doublet_detection 0
  • gender determination 0
  • ribosomal 0
  • copy number alterations 0
  • long read alignment 0
  • significance statistic 0
  • maf 0
  • construct 0
  • cellsnp 0
  • toml 0
  • nuclear segmentation 0
  • vcfbreakmulti 0
  • uniq 0
  • deduplicate 0
  • VCFtools 0
  • verifybamid 0
  • DNA contamination estimation 0
  • import segmentation 0
  • graph projection to vcf 0
  • usearch 0
  • solo 0
  • scvi 0
  • guidetree 0
  • http(s) 0
  • utility 0
  • sintax 0
  • vsearch/sort 0
  • p-value 0
  • grea 0
  • regtools 0
  • plotting 0
  • paired reads re-pairing 0
  • patterns 0
  • SMN1 0
  • SMN2 0
  • POA 0
  • sniffles 0
  • core 0
  • snippy 0
  • dist 0
  • hashing-based deconvoltion 0
  • regex 0
  • fix 0
  • autofluorescence 0
  • malformed 0
  • InterProScan 0
  • partitioning 0
  • chip 0
  • dbnsfp 0
  • predictions 0
  • updatedata 0
  • run 0
  • pdb 0
  • SNPs 0
  • CRAM 0
  • gnu 0
  • busco 0
  • sha256 0
  • relative coverage 0
  • lifestyle 0
  • MMseqs2 0
  • catpack 0
  • rare variants 0
  • error 0
  • transposable element 0
  • de-novo 0
  • Computational Immunology 0
  • longread 0
  • generic 0
  • sliding window 0
  • 256 bit 0
  • Bioinformatics Tools 0
  • Immune Deconvolution 0
  • shinyngs 0
  • doublet 0
  • exploratory 0
  • boxplot 0
  • density 0
  • features 0
  • coreutils 0
  • hamming-distance 0
  • invariant 0
  • fast5 0
  • recovery 0
  • ATLAS 0
  • detecting svs 0
  • short-read sequencing 0
  • lexogen 0
  • sylph 0
  • mgi 0
  • sequencing_bias 0
  • svtk/baftest 0
  • baftest 0
  • countsvtypes 0
  • genotype-based demultiplexing 0
  • variantcalling 0
  • donor deconvolution 0
  • rdtest2vcf 0
  • rdtest 0
  • split_kmers 0
  • vcf2bed 0
  • leafcutter 0
  • decompress 0
  • post mortem damage 0
  • polya tail 0
  • mapad 0
  • bias 0
  • sccmec 0
  • constant 0
  • overlap-based merging 0
  • cycif 0
  • background 0
  • single-stranded 0
  • ancientDNA 0
  • rRNA 0
  • ribosomal RNA 0
  • check 0
  • authentict 0
  • block substitutions 0
  • decomposeblocksub 0
  • signatures 0
  • streptococcus 0
  • hash sketch 0
  • identity-by-descent 0
  • fracminhash sketch 0
  • read group 0
  • paired reads merging 0
  • translation 0
  • spatype 0
  • functional enrichment 0
  • spa 0
  • droplet based single cells 0
  • geo 0
  • c to t 0
  • adna 0
  • script 0
  • standard 0
  • clahe 0
  • install 0
  • joint-genotyping 0
  • genotypegvcf 0
  • realign 0
  • model 0
  • svg 0
  • xml 0
  • circular 0
  • spot 0
  • introns 0
  • java 0
  • rank 0
  • AMPs 0
  • parallel 0
  • hashing-based deconvolution 0
  • Staphylococcus aureus 0
  • plastid 0
  • tag2tag 0
  • resfinder 0
  • resistance genes 0
  • haplotag 0
  • quality check 0
  • raw 0
  • association 0
  • bam2fastx 0
  • bam2fastq 0
  • immcantation 0
  • airrseq 0
  • immunoinformatics 0
  • co-orthology 0
  • homology 0
  • sequence similarity 0
  • spectral clustering 0
  • comparative genomics 0
  • microRNA 0
  • size 0
  • deep variant 0
  • mutect 0
  • idx 0
  • affy 0
  • refresh 0
  • cram-size 0
  • Staging 0
  • staging 0
  • transform 0
  • gaps 0
  • genetic sex 0
  • multiqc 0
  • reference-independent 0
  • homologs 0
  • antimicrobial peptide prediction 0
  • nanoq 0
  • multi-tool 0
  • predict 0
  • amp 0
  • redundant 0
  • hardy-weinberg 0
  • hwe statistics 0
  • hwe equilibrium 0
  • genotype likelihood 0
  • Read filters 0
  • collapse 0
  • WGS 0
  • cgMLST 0
  • liftover 0
  • probabilistic realignment 0
  • extraction 0
  • seqfu 0
  • n50 0
  • cell_type_identification 0
  • featuretable 0
  • nucleotide sequence 0
  • Read trimming 0
  • python 0
  • parquet 0
  • functional 0
  • orthogroup 0
  • parser 0
  • dbsnp 0
  • standardize 0
  • orthologs 0
  • quarto 0
  • Illumina 0
  • uniques 0
  • r 0
  • distance-based 0
  • coexpression 0
  • correlation 0
  • corpcor 0
  • assay 0
  • phylogenetics 0
  • machine_learning 0
  • drug categorization 0
  • Read report 0
  • cell_phenotyping 0
  • minimum_evolution 0
  • structural variant 0
  • GWAS 0
  • mass spectrometry 0
  • Escherichia coli 0
  • mygene 0
  • elprep 0
  • chloroplast 0
  • confidence 0
  • blat 0
  • alr 0
  • clr 0
  • elfasta 0
  • boxcox 0
  • retrieval 0
  • nucleotide content 0
  • tnscope 0
  • AT content 0
  • cell_barcodes 0
  • nucBed 0
  • bclconvert 0
  • tag 0
  • prior knowledge 0
  • propd 0
  • transcription factors 0
  • Read coverage histogram 0
  • biological activity 0
  • bgen 0
  • groupby 0
  • targz 0
  • workflow_mode 0
  • admixture 0
  • proteus 0
  • readproteingroups 0
  • reference panels 0
  • eigenvectors 0
  • hicPCA 0
  • sliding 0
  • quality_control 0
  • snakemake 0
  • workflow 0
  • 10x 0
  • controlstatistics 0
  • regulatory network 0
  • createreadcountpanelofnormals 0
  • copyratios 0
  • denoisereadcounts 0
  • readwriter 0
  • dnamodelapply 0
  • dnascope 0
  • go 0
  • emoji 0
  • source tracking 0
  • omics 0
  • tarball 0
  • mass_error 0
  • array_cgh 0
  • ancestral alleles 0
  • derived alleles 0
  • fastqfilter 0
  • tnfilter 0
  • nuclear contamination estimate 0
  • paraphase 0
  • vsearch/fastqfilter 0
  • vsearch/dereplicate 0
  • telseq 0
  • stardist 0
  • ATACseq 0
  • cytosure 0
  • post Post-processing 0
  • vector 0
  • gprofiler2 0
  • gost 0
  • variant-calling 0
  • case/control 0
  • poolseq 0
  • search engine 0
  • rad 0
  • site frequency spectrum 0
  • allele counts 0
  • tar 0
  • Bayesian 0
  • reverse complement 0
  • simulation 0
  • hmmfetch 0
  • decompose 0
  • translate 0
  • structural-variants 0
  • transmembrane 0
  • jvarkit 0
  • genome graph 0
  • tnseq 0
  • shift 0
  • scimap 0
  • spatial_neighborhoods 0
  • decoy 0
  • associations 0
  • htseq 0
  • rrna 0
  • installation 0
  • sompy 0
  • doCounts 0
  • ATACshift 0
  • peak picking 0
  • mgf 0
  • amino acid 0
  • sex determination 0
  • genomes on a tree 0
  • genome manipulation 0
  • genome statistics 0
  • crispr 0
  • gget 0
  • low coverage 0
  • antibody capture 0
  • antigen capture 0
  • Sample 0
  • Haplotypes 0
  • Imputation 0
  • joint-variant-calling 0
  • GNU 0
  • merge compare 0
  • multiomics 0
  • gfastats 0
  • tama_collapse.py 0
  • mkvdjref 0
  • gene model 0
  • TAMA 0
  • gstama/merge 0
  • gstama/polyacleanup 0
  • GTDB taxonomy 0
  • genome taxonomy database 0
  • archaea 0
  • cellpose 0
  • gunc 0
  • gunzip 0
  • gvcftools 0
  • extract_variants 0
  • genome summary 0
  • hifi 0
  • variantrecalibrator 0
  • reblockgvcf 0
  • revert 0
  • selectvariants 0
  • shiftchain 0
  • shiftfasta 0
  • shiftintervals 0
  • site depth 0
  • splitcram 0
  • splitintervals 0
  • svannotate 0
  • svcluster 0
  • variantfiltration 0
  • recalibration model 0
  • gawk 0
  • txt 0
  • file parsing 0
  • bgc 0
  • chromosome_visualization 0
  • duplicate removal 0
  • genome profile 0
  • compound 0
  • models 0
  • chromap 0
  • genome size 0
  • genome heterozygosity 0
  • repeat content 0
  • Salmonella Typhi 0
  • Mykrobe 0
  • extractvariants 0
  • abricate 0
  • printreads 0
  • Salmonella enterica 0
  • population genomics 0
  • interproscan 0
  • genomic islands 0
  • insertion 0
  • jasminesv 0
  • jasmine 0
  • Python 0
  • Jupyter 0
  • jupytext 0
  • papermill 0
  • tblastn 0
  • subtyping 0
  • kallisto/index 0
  • pixel_classification 0
  • quant 0
  • sorted 0
  • digital normalization 0
  • k-mer counting 0
  • effective genome size 0
  • Klebsiella 0
  • pneumoniae 0
  • file manipulation 0
  • kegg 0
  • kofamscan 0
  • bioawk 0
  • subtract 0
  • probability_maps 0
  • pixel classification 0
  • amrfinderplus 0
  • gccounter 0
  • fARGene 0
  • rgi 0
  • ibd 0
  • hbd 0
  • beagle 0
  • mitochondrial 0
  • haplogroups 0
  • Assembly 0
  • Haemophilus influenzae 0
  • haplotype resolution 0
  • domains 0
  • compartments 0
  • topology 0
  • calder2 0
  • readcounter 0
  • multicut 0
  • cadd 0
  • reformat 0
  • HMMER 0
  • Hidden Markov Model 0
  • hmtnote 0
  • annotations 0
  • pos 0
  • haemophilus 0
  • panel_of_normals 0
  • IDR 0
  • igv 0
  • igv.js 0
  • js 0
  • genome browser 0
  • printsvevidence 0
  • spliced 0
  • SRA 0
  • TMA dearray 0
  • UNet 0
  • str 0
  • faqcs 0
  • antibiotic resistance genes 0
  • ARGs 0
  • ANI 0
  • ENA 0
  • Cores 0
  • public 0
  • consensus sequence 0
  • duplexumi 0
  • groupreads 0
  • unmapped 0
  • ubam 0
  • zipperbams 0
  • single molecule 0
  • generate 0
  • random 0
  • Segmentation 0
  • cache 0
  • lint 0
  • PEP 0
  • corrrelation 0
  • scatterplot 0
  • cumulative coverage 0
  • paired-end 0
  • pcr duplicates 0
  • cutesv 0
  • blastx 0
  • gct 0
  • segment 0
  • cls 0
  • duphold 0
  • structural variation 0
  • depth information 0
  • escherichia coli 0
  • schema 0
  • percent on target 0
  • pep 0
  • eigenstratdatabasetools 0
  • eklipse 0
  • na 0
  • version 0
  • circos 0
  • deletion 0
  • custom 0
  • split by chromosome 0
  • embl 0
  • genbank 0
  • swissprot 0
  • Streptococcus pyogenes 0
  • endogenous DNA 0
  • partition histograms 0
  • fq 0
  • postprocessgermlinecnvcalls 0
  • genomicsdb 0
  • dragstr 0
  • condensedepthevidence 0
  • createsequencedictionary 0
  • polymut 0
  • createsomaticpanelofnormals 0
  • determinegermlinecontigploidy 0
  • duplication metrics 0
  • estimatelibrarycomplexity 0
  • filterintervals 0
  • splice 0
  • filtervarianttranches 0
  • tranche filtering 0
  • gatherbqsrreports 0
  • genomicsdbimport 0
  • jointgenotyping 0
  • panelofnormalscreation 0
  • germline contig ploidy 0
  • germlinecnvcaller 0
  • germlinevariantsites 0
  • getpileupsumaries 0
  • readcountssummary 0
  • indexfeaturefile 0
  • learnreadorientationmodel 0
  • readorientationartifacts 0
  • leftalignandtrimvariants 0
  • mergebamalignment 0
  • mutectstats 0
  • snvs 0
  • composestrtablefile 0
  • rust 0
  • targets 0
  • variant caller 0
  • target 0
  • somatic variant calling 0
  • germline variant calling 0
  • bacterial variant calling 0
  • export 0
  • UShER 0
  • gamma 0
  • gene-calling 0
  • gangstr 0
  • access 0
  • heattree 0
  • annotateintervals 0
  • polymorphic 0
  • cmseq 0
  • protein coding genes 0
  • polymorphic sites 0
  • variant quality score recalibration 0
  • vqsr 0
  • asereadcounter 0
  • bedtointervallist 0
  • calculatecontamination 0
  • cross-samplecontamination 0
  • getpileupsummaries 0
  • calibratedragstrmodel 0
  • cnnscorevariants 0
  • collectreadcounts 0
  • collectsvevidence 0
  • reorder 0
  • train 0
  • induce 0
  • genomic intervals 0
  • microscopy 0
  • background_correction 0
  • contact 0
  • pretext 0
  • jpg 0
  • bmp 0
  • contact maps 0
  • gene finding 0
  • illumiation_correction 0
  • element 0
  • intervals coverage 0
  • trimBam 0
  • bamUtil 0
  • normal database 0
  • pmdtools 0
  • panel of normals 0
  • cutoff 0
  • haplotype purging 0
  • duplicate purging 0
  • false duplications 0
  • assembly curation 0
  • Haplotype purging 0
  • False duplications 0
  • Assembly curation 0
  • track 0
  • purging 0
  • bamtools/split 0
  • yaml 0
  • quast 0
  • porechop_abi 0
  • variant genetic 0
  • subsampling 0
  • csRNA-seq 0
  • mate-pair 0
  • liftovervcf 0
  • pcr 0
  • picard/renamesampleinvcf 0
  • sortvcf 0
  • deletions 0
  • insertions 0
  • tandem duplications 0
  • CoPRO 0
  • GRO-cap 0
  • PRO-cap 0
  • CAGE 0
  • NETCAGE 0
  • RAMPAGE 0
  • STRIPE-seq 0
  • scoring 0
  • PRO-seq 0
  • GRO-seq 0
  • genetic 0
  • deduping 0
  • smaller fastqs 0
  • clumping fastqs 0
  • exclude 0
  • variant identifiers 0
  • subset 0
  • indep 0
  • indep pairwise 0
  • recode 0
  • whole genome association 0
  • identifiers 0
  • neighbour-joining 0
  • long uncorrected reads 0
  • virulent 0
  • scramble 0
  • cluster analysis 0
  • clusteridentifier 0
  • peak-caller 0
  • cut&tag 0
  • cut&run 0
  • chromatin 0
  • seacr 0
  • bacphlip 0
  • applyvarcal 0
  • VQSR 0
  • variant recalibration 0
  • subseq 0
  • read pairs 0
  • grep 0
  • sequence headers 0
  • sertotype 0
  • interleave 0
  • temperate 0
  • header 0
  • seq 0
  • selection 0
  • random draw 0
  • pseudohaploid 0
  • pseudodiploid 0
  • freqsum 0
  • bam2seqz 0
  • gc_wiggle 0
  • readgroup 0
  • paired 0
  • rhocall 0
  • pedfilter 0
  • R 0
  • bamstat 0
  • bamtools/convert 0
  • strandedness 0
  • experiment 0
  • read_pairs 0
  • fragment_size 0
  • inner_distance 0
  • read distribution 0
  • sequence-based 0
  • mapping-based 0
  • mouse 0
  • integrity 0
  • rtg 0
  • rocplot 0
  • repair 0
  • rtg-tools 0
  • salsa 0
  • salsa2 0
  • LCA 0
  • Ancestor 0
  • multimapper 0
  • flagstat 0
  • sambamba 0
  • amplicon 0
  • ampliconclip 0
  • calmd 0
  • faidx 0
  • insert size 0
  • hybrid-selection 0
  • phylogenetic composition 0
  • adapter removal 0
  • contour map 0
  • chunking 0
  • mass-spectroscopy 0
  • mcr-1 0
  • MD5 0
  • 128 bit 0
  • megahit 0
  • denovo 0
  • debruijn 0
  • daa 0
  • rma6 0
  • Neisseria meningitidis 0
  • k-mer frequency 0
  • 3D heat map 0
  • Merqury 0
  • maskfasta 0
  • jaccard 0
  • assembly evaluation 0
  • smudgeplot 0
  • ploidy 0
  • unionsum 0
  • metaphlan 0
  • methylation bias 0
  • mbias 0
  • assembler 0
  • de Bruijn 0
  • overlap 0
  • microrna 0
  • getfasta 0
  • target prediction 0
  • reference genome 0
  • sgRNA 0
  • collapsing 0
  • legionella 0
  • clinical 0
  • pneumophila 0
  • limma 0
  • Listeria monocytogenes 0
  • slopBed 0
  • lofreq/call 0
  • lofreq/filter 0
  • qualities 0
  • AMP 0
  • peptide prediction 0
  • bases 0
  • functional genomics 0
  • CRISPR-Cas9 0
  • representations 0
  • maximum-likelihood 0
  • rra 0
  • sizes 0
  • region 0
  • shiftBed 0
  • DNA damage 0
  • NGS 0
  • damage patterns 0
  • multinterval 0
  • estimate 0
  • taxonomic assignment 0
  • mash/sketch 0
  • reduced 0
  • mitochondrial genome 0
  • genomecov 0
  • illumina datasets 0
  • select 0
  • tumor/normal 0
  • hla-typing 0
  • ILP 0
  • HLA-I 0
  • block-compressed 0
  • update header 0
  • PCR/optical duplicates 0
  • flip 0
  • upper-triangular matrix 0
  • ligation junctions 0
  • pairtools 0
  • pairstools 0
  • restriction fragments 0
  • BCF 0
  • graph formats 0
  • graphs 0
  • subreads 0
  • pbp 0
  • pair-end 0
  • read 0
  • pedigrees 0
  • motif 0
  • ChIP-Seq 0
  • phantom peaks 0
  • prophage 0
  • identification 0
  • graph viz 0
  • graph unchopping 0
  • closest 0
  • contaminant 0
  • bamtobed 0
  • mosdepth 0
  • otu table 0
  • sorting 0
  • microsatellite instability 0
  • scan 0
  • mtnucratio 0
  • ratio 0
  • autozygosity 0
  • mitochondrial to nuclear ratio 0
  • bioinformatics tools 0
  • Beautiful stand-alone HTML report 0
  • GATK UnifiedGenotyper 0
  • SNP table 0
  • cancer genome 0
  • somatic structural variations 0
  • mobile element insertions 0
  • sequencing summary 0
  • NextGenMap 0
  • ngm 0
  • Neisseria gonorrhoeae 0
  • gender 0
  • homozygosity 0
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  • graph construction 0
  • graph drawing 0
  • prepare 0

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

agat:

Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.

Converts certain output formats to VCF

012010

vcf_gz vcf bcf_gz bcf hap legend samples tbi csi versions

bcftools:

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.

Index VCF tools

01

csi tbi versions

bcftools:

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.

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:

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 plugin impute-info:

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

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:

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 plugin setGT:

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.

combines overlapping or โ€œbook-endedโ€ features in an interval file into a single feature which spans all of the combined features.

01

bed versions

bedtools:

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

bedtools:

A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.

Combine output of metagenomic samples analyzed by bracken.

01

txt versions

bracken:

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.

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

checkm:

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

checkm:

Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes.

CheckM2 database download

0

database versions

checkm2:

CheckM2 - Rapid assessment of genome bin quality using machine learning

CheckM2 bin quality prediction

0101

checkm2_output checkm2_tsv versions

checkm2:

CheckM2 - Rapid assessment of genome bin quality using machine learning

binning of metagenomic sequences

01

fasta bins fm index links result versions

Predict recomination events in bacterial genomes

012

emsim em status newick fasta pos_ref versions

Derive off-target (โ€œantitargetโ€) bins from target regions.

01

bed versions

cnvkit:

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.

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

concoct:

Clustering cONtigs with COverage and ComposiTion

Generate the input coverage table for CONCOCT using a BEDFile

0123

tsv versions

concoct:

Clustering cONtigs with COverage and ComposiTion

Cut up fasta file in non-overlapping or overlapping parts of equal length.

010

fasta bed versions

concoct:

Clustering cONtigs with COverage and ComposiTion

Creates a FASTA file for each new cluster assigned by CONCOCT

012

fasta versions

concoct:

Clustering cONtigs with COverage and ComposiTion

Merge consecutive parts of the original contigs original cut up by cut_up_fasta.py

01

csv versions

concoct:

Clustering cONtigs with COverage and ComposiTion

Run matrix balancing on a cool file

012

cool versions

cooler:

Sparse binary format for genomic interaction matrices

Create a cooler from genomic pairs and bins

01230

cool versions

cooler:

Sparse binary format for genomic interaction matrices

Generate fragment-delimited genomic bins

000

bed versions

cooler:

Sparse binary format for genomic interaction matrices

Dump a coolerโ€™s data to a text stream.

012

bedpe versions

cooler:

Sparse binary format for genomic interaction matrices

Generate fixed-width genomic bins

012

bed versions

cooler:

Sparse binary format for genomic interaction matrices

Merge multiple coolers with identical axes

01

cool versions

cooler:

Sparse binary format for genomic interaction matrices

Generate a multi-resolution cooler file by coarsening

01

mcool versions

cooler:

Sparse binary format for genomic interaction matrices

DAS Tool binning step.

01230

log summary contig2bin eval bins pdfs fasta_proteins candidates_faa fasta_archaea_scg fasta_bacteria_scg b6 seqlength versions

dastool:

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

010

fastatocontig2bin versions

dastool:

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

010

scaffolds2bin versions

dastool:

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.

Computes read coverage for genomic regions (bins) across the entire genome.

0123

matrix versions

deeptools:

A set of user-friendly tools for normalization and visualization of deep-sequencing data

runs a differential expression analysis with DESeq2

01230120101

results dispersion_plot rdata size_factors normalised_counts rlog_counts vst_counts model session_info versions

deseq2:

Differential gene expression analysis based on the negative binomial distribution

Searches a term in a public NCBI database

010

xml versions

entrezdirect:

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

entrezdirect:

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

entrezdirect:

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.

Perform merging of mate paired-end sequencing reads

01

merged notcombined histogram 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:

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

Combine per-sample gVCF files produced by HaplotypeCaller into a multi-sample gVCF file

012000

combined_gvcf versions

gatk4:

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.

Prepares bins for coverage collection.

0101010101

interval_list versions

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.

Compare, merge, annotate and estimate accuracy of generated gtf files

0101201

annotated_gtf combined_gtf tmap refmap loci stats tracking versions

Compute the r2 correlation between imputed dosages (in MAF bins) and highly-confident genotype calls from the high-coverage dataset.

01234567000

errors_cal errors_grp errors_spl rsquare_grp rsquare_spl versions

glimpse:

GLIMPSE 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:

GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies.

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:

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

Quickly generate evenly sized (by amount of data) regions across a number of bam/cram files

01010

bed versions

goleft:

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

Tools for population-scale genotyping using pangenome graphs.

01

vcf tbi versions

graphtyper:

A graph-based variant caller capable of genotyping population-scale short read data sets while incorporating previously discovered variants.

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

Tool to summarize and combine all hAMRonization reports into a single file

00

json tsv html versions

hamronization:

Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification

Create a tag directory with the HOMER suite

010

tagdir taginfo versions

homer:

HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.

samtools:

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.

DESeq2:

Differential gene expression analysis based on the negative binomial distribution

edgeR:

Empirical Analysis of Digital Gene Expression Data in R

Takes multiple kraken-style reports and combines them into a single report file

01

txt versions

krakentools:

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.

MaxBin is a software that is capable of clustering metagenomic contigs

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binned_fastas summary abundance log marker_counts unbinned_fasta tooshort_fasta marker_bins marker_genes versions

Depth computation per contig step of metabat2

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depth versions

metabat2:

Metagenome binning

Metagenome binning of contigs

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tooshort lowdepth unbinned membership fasta versions

metabat2:

Metagenome binning

Squeezes multiple graphs in ODGI format into the same file in ODGI format.

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graph versions

odgi:

An optimized dynamic genome/graph implementation

Metrics describing a variation graph and its path relationship.

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tsv yaml versions

odgi:

An optimized dynamic genome/graph implementation

Determines the depth in a BAM/CRAM file

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depth binned_depth versions

paragraph:

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

pbbam:

PacBio BAM C++ library

Minimalistic tool which creates an index file that enables random access into PacBio BAM files

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pbi versions

pbtk:

pbtk - PacBio BAM toolkit

Analyses binary variant call format (BCF) files using plink

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bed bim fam versions

plink:

Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

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

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

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bam versions

metagenomic binning with self-supervised learning

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csv model output_fasta recluster_fasta tsv versions

semibin:

Metagenomic binning with semi-supervised siamese neural network

Count reads that map to genomic features

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counts summary versions

featurecounts:

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.

Transcript Selector for BRAKER TSEBRA combines gene predictions by selecting transcripts based on their extrisic evidence support

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tsebra_gtf tsebra_scores versions

Convert ascii format wig file to binary big wig format

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bw versions

ucsc:

Convert ascii format wig file (in fixedStep, variableStep or bedGraph format) to binary big wig format

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

varlociraptor:

Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control.

Extracting sequences that were unbinnned by vRhyme into a FASTA file

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unbinned_sequences versions

vrhyme:

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:

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:

vRhyme functions by utilizing coverage variance comparisons and supervised machine learning classification of sequence features to construct viral metagenome-assembled genomes (vMAGs).

Find copy number aberrations

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aberrations_bed bins_bed segments_bed chr_statistics chr_plots genome_plot versions

wisecondorx:

WIthin-SamplE COpy Number aberration DetectOR, including sex chromosomes

Performs assembly scaffolding using YaHS

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scaffolds_fasta scaffolds_agp binary versions

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