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.

  • bam 37
  • fastq 35
  • fasta 34
  • reference 33
  • map 28
  • index 26
  • genome 24
  • align 18
  • sentieon 17
  • alignment 16
  • metagenomics 14
  • sam 14
  • genomics 12
  • vcf 11
  • mapping 10
  • bisulfite 8
  • bisulphite 8
  • methylseq 8
  • methylation 8
  • 5mC 8
  • pairs 8
  • mappability 8
  • bwa 8
  • cram 7
  • bismark 7
  • sort 6
  • classify 6
  • structural variants 5
  • qc 5
  • gtf 5
  • taxonomic profiling 5
  • wgs 5
  • sequences 5
  • kmers 5
  • short-read 5
  • mem 5
  • annotation 4
  • merge 4
  • filter 4
  • coverage 4
  • ancient DNA 4
  • palaeogenomics 4
  • archaeogenomics 4
  • dedup 4
  • deduplication 4
  • 3-letter genome 4
  • ptr 4
  • coptr 4
  • quality control 3
  • somatic 3
  • taxonomy 3
  • isoseq 3
  • rnaseq 3
  • stats 3
  • aDNA 3
  • genotype 3
  • aligner 3
  • splicing 3
  • counts 3
  • wxs 3
  • ont 3
  • variant_calling 3
  • mapper 3
  • pairsam 3
  • long_read 3
  • panel 3
  • minimap2 3
  • uLTRA 3
  • spaceranger 3
  • small indels 3
  • aln 3
  • bed 2
  • gatk4 2
  • variant calling 2
  • variants 2
  • cnv 2
  • count 2
  • clustering 2
  • trimming 2
  • kmer 2
  • consensus 2
  • bqsr 2
  • metrics 2
  • matrix 2
  • damage 2
  • long reads 2
  • mkref 2
  • umi 2
  • germline 2
  • spatial 2
  • report 2
  • bedGraph 2
  • deamination 2
  • microbiome 2
  • miscoding lesions 2
  • circrna 2
  • fgbio 2
  • archaeogenetics 2
  • bedgraph 2
  • palaeogenetics 2
  • umitools 2
  • malt 2
  • hmmcopy 2
  • bwameth 2
  • mirdeep2 2
  • RNA sequencing 2
  • mapcounter 2
  • tnhaplotyper2 2
  • varcal 2
  • fusions 2
  • soft-clipped clusters 2
  • metamaps 2
  • gem 2
  • heatmap 2
  • assembly 1
  • database 1
  • gff 1
  • bacteria 1
  • statistics 1
  • split 1
  • classification 1
  • pacbio 1
  • convert 1
  • conversion 1
  • VCF 1
  • bedtools 1
  • phylogeny 1
  • gvcf 1
  • sv 1
  • build 1
  • cna 1
  • picard 1
  • imaging 1
  • DNA methylation 1
  • haplotype 1
  • scWGBS 1
  • WGBS 1
  • base quality score recalibration 1
  • plot 1
  • filtering 1
  • db 1
  • biscuit 1
  • samtools 1
  • transcript 1
  • bisulfite sequencing 1
  • gene 1
  • gff3 1
  • segmentation 1
  • example 1
  • newick 1
  • duplicates 1
  • merging 1
  • summary 1
  • single cell 1
  • query 1
  • indels 1
  • csv 1
  • sourmash 1
  • clipping 1
  • haplotypecaller 1
  • gsea 1
  • hic 1
  • profile 1
  • compare 1
  • enrichment 1
  • paf 1
  • DNA sequencing 1
  • targeted sequencing 1
  • hybrid capture sequencing 1
  • copy number alteration calling 1
  • normalization 1
  • sketch 1
  • preprocessing 1
  • pseudoalignment 1
  • PacBio 1
  • miRNA 1
  • transcripts 1
  • indel 1
  • duplication 1
  • UMI 1
  • scores 1
  • quality trimming 1
  • adapter trimming 1
  • clean 1
  • RNA-seq 1
  • image 1
  • hi-c 1
  • atac-seq 1
  • chip-seq 1
  • chromosome 1
  • intervals 1
  • wig 1
  • png 1
  • C to T 1
  • frame-shift correction 1
  • long-read sequencing 1
  • GC content 1
  • import 1
  • bfiles 1
  • minhash 1
  • hlala_typing 1
  • instrain 1
  • hla_typing 1
  • maximum likelihood 1
  • hlala 1
  • hla 1
  • gene set 1
  • sequence analysis 1
  • cnvnator 1
  • mitochondrion 1
  • orthology 1
  • fixmate 1
  • ancient dna 1
  • spatial_omics 1
  • gene set analysis 1
  • realignment 1
  • joint genotyping 1
  • parse 1
  • htseq 1
  • tnfilter 1
  • tnseq 1
  • tnscope 1
  • chloroplast 1
  • UNet 1
  • TMA dearray 1
  • Segmentation 1
  • Cores 1
  • umicollapse 1
  • mapad 1
  • adna 1
  • c to t 1
  • unmapped 1
  • groupreads 1
  • readwriter 1
  • dnamodelapply 1
  • dnascope 1
  • ubam 1
  • VCFtools 1
  • zipperbams 1
  • long read alignment 1
  • pangenome-scale 1
  • all versus all 1
  • mashmap 1
  • wavefront 1
  • HLA 1
  • corrrelation 1
  • paired reads re-pairing 1
  • scatterplot 1
  • paired reads merging 1
  • scimap 1
  • liftover 1
  • spatial_neighborhoods 1
  • overlap-based merging 1
  • realign 1
  • circular 1
  • bwamem2 1
  • bwameme 1
  • variantcalling 1
  • mergebamalignment 1
  • k-mer frequency 1
  • 3D heat map 1
  • contour map 1
  • pairtools 1
  • pairstools 1
  • restriction fragments 1
  • select 1
  • upper-triangular matrix 1
  • ligation junctions 1
  • flip 1
  • NextGenMap 1
  • ngm 1
  • PCR/optical duplicates 1
  • chromap 1
  • pixel_classification 1
  • probability_maps 1
  • population genomics 1
  • insertion 1
  • Mykrobe 1
  • Salmonella Typhi 1
  • duplicate removal 1
  • DNA damage 1
  • NGS 1
  • damage patterns 1
  • CRISPR-Cas9 1
  • sgRNA 1
  • functional genomics 1
  • VQSR 1
  • variant recalibration 1
  • applyvarcal 1
  • annotateintervals 1
  • insert size 1
  • repair 1
  • paired 1
  • read pairs 1
  • scramble 1
  • cluster analysis 1
  • clusteridentifier 1
  • ribosomal RNA 1
  • rRNA 1
  • signatures 1
  • recode 1
  • whole genome association 1
  • contact 1
  • pretext 1
  • jpg 1
  • bmp 1
  • contact maps 1
  • clumping fastqs 1
  • deduping 1
  • smaller fastqs 1
  • multimapper 1
  • mapping-based 1
  • read distribution 1
  • sequence-based 1
  • LCA 1
  • Ancestor 1
  • normal database 1
  • panel of normals 1
  • download 0
  • nanopore 0
  • MSA 0
  • gfa 0
  • k-mer 0
  • variant 0
  • contamination 0
  • quality 0
  • binning 0
  • proteomics 0
  • single-cell 0
  • copy number 0
  • imputation 0
  • contigs 0
  • graph 0
  • bcftools 0
  • variation graph 0
  • reporting 0
  • compression 0
  • databases 0
  • protein 0
  • illumina 0
  • table 0
  • indexing 0
  • QC 0
  • demultiplex 0
  • antimicrobial resistance 0
  • visualisation 0
  • long-read 0
  • phage 0
  • tsv 0
  • openms 0
  • serotype 0
  • searching 0
  • protein sequence 0
  • histogram 0
  • pangenome graph 0
  • markduplicates 0
  • bins 0
  • amr 0
  • depth 0
  • cluster 0
  • structure 0
  • neural network 0
  • expression 0
  • mags 0
  • LAST 0
  • checkm 0
  • metagenome 0
  • completeness 0
  • iCLIP 0
  • repeat 0
  • mmseqs2 0
  • annotate 0
  • virus 0
  • bcf 0
  • machine learning 0
  • validation 0
  • low-coverage 0
  • cooler 0
  • mag 0
  • decompression 0
  • peaks 0
  • transcriptome 0
  • msa 0
  • population genetics 0
  • kraken2 0
  • glimpse 0
  • blast 0
  • evaluation 0
  • hmmsearch 0
  • genotyping 0
  • phasing 0
  • ucsc 0
  • sequence 0
  • complexity 0
  • ncbi 0
  • seqkit 0
  • differential 0
  • tumor-only 0
  • demultiplexing 0
  • antimicrobial resistance genes 0
  • prediction 0
  • mirna 0
  • vsearch 0
  • json 0
  • antimicrobial peptides 0
  • prokaryote 0
  • low frequency variant calling 0
  • scRNA-seq 0
  • cnvkit 0
  • pangenome 0
  • plasmid 0
  • gzip 0
  • NCBI 0
  • taxonomic classification 0
  • mitochondria 0
  • hmmer 0
  • multiple sequence alignment 0
  • feature 0
  • single 0
  • snp 0
  • amps 0
  • detection 0
  • kallisto 0
  • adapters 0
  • benchmark 0
  • gridss 0
  • svtk 0
  • de novo 0
  • arg 0
  • fragment 0
  • call 0
  • visualization 0
  • isolates 0
  • mutect2 0
  • view 0
  • idXML 0
  • antibiotic resistance 0
  • interval 0
  • mpileup 0
  • extract 0
  • diversity 0
  • tabular 0
  • riboseq 0
  • text 0
  • de novo assembly 0
  • MAF 0
  • profiling 0
  • CLIP 0
  • ganon 0
  • bcl2fastq 0
  • STR 0
  • bin 0
  • snps 0
  • interval_list 0
  • cut 0
  • genome assembler 0
  • diamond 0
  • bigwig 0
  • deep learning 0
  • structural 0
  • compress 0
  • peak-calling 0
  • public datasets 0
  • phylogenetic placement 0
  • read depth 0
  • ranking 0
  • genmod 0
  • SV 0
  • cat 0
  • chunk 0
  • ATAC-seq 0
  • FASTQ 0
  • concatenate 0
  • fastx 0
  • sample 0
  • sequencing 0
  • add 0
  • resistance 0
  • union 0
  • ampir 0
  • xeniumranger 0
  • ancestry 0
  • pypgx 0
  • isomir 0
  • microarray 0
  • parsing 0
  • retrotransposon 0
  • fungi 0
  • telomere 0
  • redundancy 0
  • BGC 0
  • biosynthetic gene cluster 0
  • propr 0
  • logratio 0
  • family 0
  • bgzip 0
  • ccs 0
  • DNA sequence 0
  • reference-free 0
  • microsatellite 0
  • reads 0
  • quantification 0
  • ngscheckmate 0
  • containment 0
  • matching 0
  • HiFi 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
  • krona chart 0
  • npz 0
  • typing 0
  • entrez 0
  • guide tree 0
  • covid 0
  • organelle 0
  • transcriptomics 0
  • repeat expansion 0
  • fcs-gx 0
  • chimeras 0
  • fingerprint 0
  • PCA 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
  • vrhyme 0
  • untar 0
  • archiving 0
  • plink2 0
  • rsem 0
  • wastewater 0
  • genome assembly 0
  • polishing 0
  • mlst 0
  • spark 0
  • prokka 0
  • dictionary 0
  • fam 0
  • bim 0
  • insert 0
  • score 0
  • replace 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
  • tabix 0
  • subsample 0
  • informative sites 0
  • kinship 0
  • identity 0
  • relatedness 0
  • lossless 0
  • observations 0
  • shapeit 0
  • zip 0
  • gene expression 0
  • image_analysis 0
  • pileup 0
  • bamtools 0
  • host 0
  • bakta 0
  • cellranger 0
  • mcmicro 0
  • ataqv 0
  • complement 0
  • arriba 0
  • fusion 0
  • eukaryotes 0
  • prokaryotes 0
  • cut up 0
  • cool 0
  • genome mining 0
  • angsd 0
  • remove 0
  • roh 0
  • CRISPR 0
  • bracken 0
  • mkfastq 0
  • nucleotide 0
  • kraken 0
  • microbes 0
  • abundance 0
  • checkv 0
  • rna 0
  • combine 0
  • comparisons 0
  • fai 0
  • converter 0
  • dump 0
  • highly_multiplexed_imaging 0
  • amplify 0
  • virulence 0
  • das tool 0
  • das_tool 0
  • deeparg 0
  • genomes 0
  • neubi 0
  • DRAMP 0
  • prefetch 0
  • macrel 0
  • msisensor-pro 0
  • micro-satellite-scan 0
  • removal 0
  • gwas 0
  • tumor 0
  • nextclade 0
  • msi 0
  • Pharmacogenetics 0
  • instability 0
  • MSI 0
  • homoploymer 0
  • spatial_transcriptomics 0
  • resolve_bioscience 0
  • profiles 0
  • intersection 0
  • smrnaseq 0
  • lift 0
  • graph layout 0
  • MCMICRO 0
  • Duplication purging 0
  • purge duplications 0
  • trim 0
  • library 0
  • preseq 0
  • adapter 0
  • ome-tif 0
  • variant pruning 0
  • reheader 0
  • concat 0
  • read-group 0
  • tbi 0
  • ped 0
  • intersect 0
  • GPU-accelerated 0
  • normalize 0
  • norm 0
  • scatter 0
  • windows 0
  • megan 0
  • checksum 0
  • proteome 0
  • ichorcna 0
  • cleaning 0
  • hidden Markov model 0
  • trgt 0
  • corrupted 0
  • mask 0
  • nacho 0
  • nanostring 0
  • mRNA 0
  • trancriptome 0
  • tama 0
  • gstama 0
  • immunoprofiling 0
  • iphop 0
  • refine 0
  • interactive 0
  • tree 0
  • contig 0
  • mash 0
  • lofreq 0
  • serogroup 0
  • barcode 0
  • primer 0
  • pharmacogenetics 0
  • pair 0
  • doublets 0
  • krakenuniq 0
  • screening 0
  • krakentools 0
  • screen 0
  • khmer 0
  • bustools 0
  • awk 0
  • anndata 0
  • BAM 0
  • blastn 0
  • gene labels 0
  • polyA_tail 0
  • Read depth 0
  • repeats 0
  • scaffold 0
  • interactions 0
  • rgfa 0
  • small variants 0
  • multiallelic 0
  • nucleotides 0
  • comparison 0
  • proportionality 0
  • NRPS 0
  • registration 0
  • reformatting 0
  • image_processing 0
  • RiPP 0
  • antibiotics 0
  • regression 0
  • SimpleAF 0
  • taxids 0
  • antismash 0
  • taxon name 0
  • vg 0
  • secondary metabolites 0
  • functional analysis 0
  • zlib 0
  • HOPS 0
  • leviosam2 0
  • orf 0
  • salmon 0
  • kma 0
  • long terminal retrotransposon 0
  • long terminal repeat 0
  • retrotransposons 0
  • MaltExtract 0
  • function 0
  • pharokka 0
  • bloom filter 0
  • k-mer index 0
  • COBS 0
  • archive 0
  • xz 0
  • authentication 0
  • genetics 0
  • edit distance 0
  • mudskipper 0
  • transcriptomic 0
  • parallelized 0
  • vcflib 0
  • distance 0
  • polish 0
  • xenograft 0
  • Streptococcus pneumoniae 0
  • sequenzautils 0
  • transformation 0
  • rename 0
  • seqtk 0
  • salmonella 0
  • allele 0
  • switch 0
  • dict 0
  • collate 0
  • bam2fq 0
  • dereplicate 0
  • scaffolding 0
  • graft 0
  • rtgtools 0
  • junctions 0
  • runs_of_homozygosity 0
  • shigella 0
  • differential expression 0
  • taxonomic profile 0
  • RNA-Seq 0
  • simulate 0
  • artic 0
  • aggregate 0
  • demultiplexed reads 0
  • variation 0
  • taxon tables 0
  • otu tables 0
  • standardisation 0
  • standardise 0
  • standardization 0
  • amptransformer 0
  • svdb 0
  • de novo assembler 0
  • small genome 0
  • signature 0
  • FracMinHash sketch 0
  • join 0
  • cancer genomics 0
  • snpsift 0
  • snpeff 0
  • effect prediction 0
  • ampgram 0
  • duplicate 0
  • allele-specific 0
  • short reads 0
  • reads merging 0
  • merge mate pairs 0
  • calling 0
  • cnv calling 0
  • CNV 0
  • bayesian 0
  • deconvolution 0
  • cvnkit 0
  • estimation 0
  • interval list 0
  • UMIs 0
  • filtermutectcalls 0
  • evidence 0
  • panelofnormals 0
  • recombination 0
  • eCLIP 0
  • gatk 0
  • baf 0
  • genomad 0
  • ChIP-seq 0
  • unaligned 0
  • duplex 0
  • single cells 0
  • samplesheet 0
  • regions 0
  • random forest 0
  • metagenomes 0
  • structural-variant calling 0
  • rna-seq 0
  • deseq2 0
  • blastp 0
  • fasterq-dump 0
  • eido 0
  • format 0
  • validate 0
  • fetch 0
  • eigenstrat 0
  • sra-tools 0
  • settings 0
  • emboss 0
  • correction 0
  • tab 0
  • metadata 0
  • repeat_expansions 0
  • expansionhunterdenovo 0
  • identifier 0
  • metagenomic 0
  • GEO 0
  • genome bins 0
  • microbial 0
  • concordance 0
  • phase 0
  • vdj 0
  • hmtnote 0
  • ancestral alleles 0
  • hifi 0
  • rrna 0
  • installation 0
  • sompy 0
  • doCounts 0
  • extractvariants 0
  • peak picking 0
  • allele counts 0
  • site frequency spectrum 0
  • derived alleles 0
  • ANI 0
  • nuclear contamination estimate 0
  • ARGs 0
  • antibiotic resistance genes 0
  • faqcs 0
  • array_cgh 0
  • cytosure 0
  • post Post-processing 0
  • vector 0
  • gprofiler2 0
  • gost 0
  • str 0
  • decoy 0
  • genome graph 0
  • amrfinderplus 0
  • bgen 0
  • fARGene 0
  • confidence 0
  • blat 0
  • alr 0
  • clr 0
  • cooler/balance 0
  • boxcox 0
  • public 0
  • Escherichia coli 0
  • propd 0
  • rad 0
  • Read coverage histogram 0
  • abricate 0
  • ENA 0
  • SRA 0
  • reverse complement 0
  • simulation 0
  • hmmfetch 0
  • decompose 0
  • cload 0
  • digest 0
  • transmembrane 0
  • enzyme 0
  • extract_variants 0
  • makebins 0
  • gvcftools 0
  • parser 0
  • endogenous DNA 0
  • AMPs 0
  • parallel 0
  • gunzip 0
  • plastid 0
  • Streptococcus pyogenes 0
  • resfinder 0
  • resistance genes 0
  • raw 0
  • mgf 0
  • parquet 0
  • dbsnp 0
  • model 0
  • standardize 0
  • swissprot 0
  • quarto 0
  • python 0
  • r 0
  • coexpression 0
  • correlation 0
  • corpcor 0
  • assay 0
  • phylogenetics 0
  • minimum_evolution 0
  • distance-based 0
  • percent on target 0
  • cache 0
  • rgi 0
  • mcool 0
  • structural variant 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
  • genomic bins 0
  • deep variant 0
  • genotypegvcf 0
  • mutect 0
  • idx 0
  • transform 0
  • gaps 0
  • introns 0
  • Sample 0
  • install 0
  • joint-genotyping 0
  • groupby 0
  • ibd 0
  • consensus sequence 0
  • single molecule 0
  • refflat 0
  • gtftogenepred 0
  • ucsc/liftover 0
  • mkarv 0
  • fq 0
  • lint 0
  • partition histograms 0
  • random 0
  • scRNA-Seq 0
  • generate 0
  • files 0
  • bedtobigbed 0
  • haplogroups 0
  • mitochondrial 0
  • beagle 0
  • upd 0
  • uniparental 0
  • disomy 0
  • snv 0
  • downsample 0
  • downsample bam 0
  • subsample bam 0
  • vcf2db 0
  • gemini 0
  • genepred 0
  • bigbed 0
  • lua 0
  • polya tail 0
  • short-read sequencing 0
  • germline variant calling 0
  • sequencing_bias 0
  • svtk/baftest 0
  • baftest 0
  • countsvtypes 0
  • rdtest2vcf 0
  • rdtest 0
  • somatic variant calling 0
  • vcf2bed 0
  • decompress 0
  • post mortem damage 0
  • fast5 0
  • bedgraphtobigwig 0
  • target 0
  • variant caller 0
  • rust 0
  • Assembly 0
  • Mycobacterium tuberculosis 0
  • chromosomal rearrangements 0
  • eucaryotes 0
  • coding 0
  • cds 0
  • transcroder 0
  • sequencing adapters 0
  • atlas 0
  • maf 0
  • toml 0
  • homologs 0
  • eigenvectors 0
  • copy number alterations 0
  • copy number variation 0
  • yahs 0
  • geo 0
  • proteus 0
  • readproteingroups 0
  • hicPCA 0
  • gender determination 0
  • sliding 0
  • subcontigs 0
  • snakemake 0
  • workflow 0
  • workflow_mode 0
  • duplexumi 0
  • createreadcountpanelofnormals 0
  • copyratios 0
  • denoisereadcounts 0
  • copy number analysis 0
  • hbd 0
  • linkbins 0
  • vcfbreakmulti 0
  • uniq 0
  • deduplicate 0
  • verifybamid 0
  • DNA contamination estimation 0
  • concoct 0
  • construct 0
  • graph projection to vcf 0
  • nucleotide composition 0
  • http(s) 0
  • extractunbinned 0
  • utility 0
  • copy-number 0
  • sintax 0
  • vsearch/sort 0
  • usearch 0
  • whamg 0
  • wham 0
  • nucleotide sequence 0
  • antimicrobial peptide prediction 0
  • ATLAS 0
  • gstama/merge 0
  • ATACseq 0
  • shift 0
  • ATACshift 0
  • gct 0
  • blastx 0
  • setgt 0
  • jvarkit 0
  • translate 0
  • tar 0
  • tarball 0
  • targz 0
  • cutesv 0
  • vsearch/fastqfilter 0
  • GNU 0
  • bclconvert 0
  • nucBed 0
  • AT content 0
  • nucleotide content 0
  • elfasta 0
  • elprep 0
  • TAMA 0
  • controlstatistics 0
  • source tracking 0
  • emoji 0
  • quality_control 0
  • fastqfilter 0
  • vsearch/dereplicate 0
  • admixture 0
  • structural variation 0
  • Staphylococcus aureus 0
  • hashing-based deconvolution 0
  • rank 0
  • java 0
  • script 0
  • escherichia coli 0
  • xml 0
  • svg 0
  • standard 0
  • haplotag 0
  • depth information 0
  • staging 0
  • Staging 0
  • telseq 0
  • duphold 0
  • joint-variant-calling 0
  • cls 0
  • affy 0
  • microRNA 0
  • segment 0
  • multiqc 0
  • mass_error 0
  • search engine 0
  • poolseq 0
  • variant-calling 0
  • stardist 0
  • reference panels 0
  • gene model 0
  • tags 0
  • updatedata 0
  • merge compare 0
  • recovery 0
  • mgi 0
  • sylph 0
  • tama_collapse.py 0
  • genomes on a tree 0
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  • decomposeblocksub 0
  • block substitutions 0
  • pdb 0
  • run 0
  • chip 0
  • leafcutter 0
  • partitioning 0
  • malformed 0
  • fix 0
  • regex 0
  • patterns 0
  • doublet 0
  • Immune Deconvolution 0
  • Bioinformatics Tools 0
  • Computational Immunology 0
  • catpack 0
  • prepare 0
  • split_kmers 0
  • regtools 0
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  • relabel 0
  • barcodes 0
  • pcr duplicates 0
  • subsetting 0
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  • scvi 0
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  • import segmentation 0
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  • hostile 0
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  • na 0
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  • deletion 0
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  • tag 0
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  • Bayesian 0
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  • extension 0
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  • functional enrichment 0
  • translation 0
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  • check 0
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  • hwe statistics 0
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  • reference-independent 0
  • genotype likelihood 0
  • collapse 0
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  • seqfu 0
  • cell_type_identification 0
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  • embl 0
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  • split by chromosome 0
  • clahe 0
  • refresh 0
  • association 0
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  • Imputation 0
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  • Illumina 0
  • PEP 0
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  • generic 0
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  • retrieval 0
  • schema 0
  • Haplotypes 0
  • MMseqs2 0
  • InterProScan 0
  • busco 0
  • droplet based single cells 0
  • genotype-based demultiplexing 0
  • GTDB taxonomy 0
  • donor deconvolution 0
  • cellsnp 0
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  • vcflib/vcffixup 0
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  • ratio 0
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  • mitochondrial to nuclear ratio 0
  • bioinformatics tools 0
  • Beautiful stand-alone HTML report 0
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  • reference genome 0
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  • methylation bias 0
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  • assembler 0
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  • overlap 0
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  • contaminant 0
  • cancer genome 0
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  • graphs 0
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  • germline contig ploidy 0
  • BCF 0
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  • pbbam 0
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  • subreads 0
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  • read 0
  • pedigrees 0
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  • motif 0
  • ChIP-Seq 0
  • phantom peaks 0
  • somatic structural variations 0
  • readcountssummary 0
  • mobile element insertions 0
  • sequencing summary 0
  • indexfeaturefile 0
  • Neisseria gonorrhoeae 0
  • gender 0
  • homozygosity 0
  • biallelic 0
  • crispr 0
  • graph construction 0
  • graph drawing 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
  • update header 0
  • denovo 0
  • reformat 0
  • identification 0
  • amino acid 0
  • Jupyter 0
  • jupytext 0
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  • genome heterozygosity 0
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  • Salmonella enterica 0
  • kallisto/index 0
  • quant 0
  • sorted 0
  • jasmine 0
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  • models 0
  • k-mer counting 0
  • effective genome size 0
  • compound 0
  • Klebsiella 0
  • pneumoniae 0
  • file manipulation 0
  • kegg 0
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  • genome profile 0
  • combining 0
  • Python 0
  • jasminesv 0
  • HMMER 0
  • pixel classification 0
  • genome summary 0
  • pos 0
  • haemophilus 0
  • Hidden Markov Model 0
  • gfastats 0
  • panel_of_normals 0
  • IDR 0
  • igv 0
  • igv.js 0
  • js 0
  • genome browser 0
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  • repeat content 0
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  • chunking 0
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  • mcr-1 0
  • site depth 0
  • MD5 0
  • maximum-likelihood 0
  • chromosome_visualization 0
  • pneumophila 0
  • bgc 0
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  • subtract 0
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  • txt 0
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  • clinical 0
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  • Listeria monocytogenes 0
  • recalibration model 0
  • slopBed 0
  • variantfiltration 0
  • lofreq/call 0
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  • qualities 0
  • AMP 0
  • peptide prediction 0
  • bases 0
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  • illumina datasets 0
  • annotations 0
  • protein coding genes 0
  • virulent 0
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  • grep 0
  • sequence headers 0
  • polymorphic sites 0
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  • header 0
  • seq 0
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  • induce 0
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  • SNPs 0
  • invariant 0
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  • background 0
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  • export 0
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  • hash sketch 0
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  • read group 0
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  • bacterial variant calling 0
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  • streptococcus 0
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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:

arcasHLA performs high resolution genotyping for HLA class I and class II genes from RNA sequencing, supporting both paired and single-end samples.

write your description here

01

json versions

bamstats:

A command line tool to compute mapping statistics from a BAM file

Align short or PacBio reads to a reference genome using BBMap

010

bam log versions

bbmap:

BBMap is a short read aligner, as well as various other bioinformatic tools.

Adapter and quality trimming of sequencing reads

010

reads log versions

bbmap:

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:

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:

BBMap is a short read aligner, as well as various other bioinformatic tools.

Split sequencing reads by mapping them to multiple references simultaneously

0100010

index primary_fastq all_fastq stats log versions

bbmap:

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:

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:

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:

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:

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:

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:

BBMap is a short read aligner, as well as various other bioinformatic tools.

Allows one to screen for overlaps between two sets of genomic features.

01201

mapped versions

bedtools:

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

A fast, compact one-liner to produce duplicate-marked, sorted, and indexed BAM files using Biscuit

010101

bam bai versions

biscuit:

A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data

samblaster:

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:

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.

Performs alignment of BS-Seq reads using bismark

010101

bam report unmapped versions

bismark:

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:

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:

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:

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:

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:

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:

Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.

Align reads to a reference genome using bowtie

01010

bam log fastq versions

bowtie:

bowtie is a software package for mapping DNA sequences against a large reference genome, such as the human genome.

Create bowtie index for reference genome

01

index versions

bowtie:

bowtie is a software package for mapping DNA sequences against a large reference genome, such as the human genome.

Align reads to a reference genome using bowtie2

01010100

sam bam cram csi crai log fastq versions

bowtie2:

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

Find SA coordinates of the input reads for bwa short-read mapping

0101

sai versions

bwa:

BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome.

Create BWA index for reference genome

01

index versions

bwa:

BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome.

Performs fastq alignment to a fasta reference using BWA

0101010

bam cram csi crai versions

bwa:

BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome.

Convert paired-end bwa SA coordinate files to SAM format

01201

bam versions

bwa:

BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome.

Convert bwa SA coordinate file to SAM format

01201

bam versions

bwa:

BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome.

Create BWA-mem2 index for reference genome

01

index versions

bwamem2:

BWA-mem2 is a software package for mapping DNA sequences against a large reference genome, such as the human genome.

Performs fastq alignment to a fasta reference using BWA

0101010

sam bam cram crai csi versions

bwa:

BWA-mem2 is a software package for mapping DNA sequences against a large reference genome, such as the human genome.

Performs fastq alignment to a fasta reference using BWA-MEME

010101000

sam bam cram crai csi versions

bwameme:

Faster BWA-MEM2 using learned-index

Performs alignment of BS-Seq reads using bwameth

010101

bam versions

bwameth:

Fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome.

Classifies metagenomic sequence data

01000

report results sam fastq_mapped fastq_unmapped versions

centrifuge:

Centrifuge is a classifier for metagenomic sequences.

Performs preprocessing and alignment of chromatin fastq files to fasta reference files using chromap.

0101010000

bed bam tagAlign pairs versions

chromap:

Fast alignment and preprocessing of chromatin profiles

Indexes a fasta reference genome ready for chromatin profiling.

01

index versions

chromap:

Fast alignment and preprocessing of chromatin profiles

A method to improve mappings on circular genomes, using the BWA mapper.

010101

fasta elongated versions

circulargenerator:

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

circularmapper:

A method to improve mappings on circular genomes such as Mitochondria.

CNVnator is a command line tool for CNV/CNA analysis from depth-of-coverage by mapped reads.

012010101

root tab versions

cnvnator:

Tool for calling copy number variations.

Calculates peak-to-through ratio (PTR) from metagenomic sequence data

01

ptr versions

coptr:

Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reads.

Computes the coverage map along the reference genome

01

coverage versions

coptr:

Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reads.

Maps the reads to the reference database

0101

bam versions

coptr:

Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reads.

Merge reads that were mapped to multiple indices

01

bam versions

coptr:

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

010100

coverage versions

coverm:

CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications

Make a transcript/gene mapping from a GTF and cross-reference with transcript quantifications.

0101000

tx2gene versions

custom:

"Custom module to create a transcript to gene mapping from a GTF and check it against transcript quantifications"

A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage

01000

results versions

Visualises sample correlations using a compressed matrix generated by mutlibamsummary or multibigwigsummary as input.

0100

pdf matrix versions

deeptools:

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

deeptools:

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

Performs fastq alignment to a reference using DRAGMAP

0101010

sam bam cram crai csi log versions

dragmap:

Dragmap is the Dragen mapper/aligner Open Source Software.

Create DRAGEN hashtable for reference genome

01

hashmap versions

dragmap:

Dragmap is the Dragen mapper/aligner Open Source Software.

Dysgu calls structural variants (SVs) from mapped sequencing reads. It is designed for accurate and efficient detection of structural variations.

012012

vcf tbi versions

Fast genome-wide functional annotation through orthology assignment.

010001

annotations orthologs hits versions

Align reads to multiple reference genomes using fastq-screen

010

txt png html fastq versions

fastqscreen:

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.

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.

010

bam histogram versions

fgbio:

A set of tools for working with genomic and high throughput sequencing data, including UMIs

FGBIO tool to zip together an unmapped and mapped BAM to transfer metadata into the output BAM

01010101

bam versions

fgbio:

A set of tools for working with genomic and high throughput sequencing data, including UMIs

Performs local realignment around indels to correct for mapping errors

012301010101

bam versions

gatk:

The full Genome Analysis Toolkit (GATK) framework, license restricted.

Annotates intervals with GC content, mappability, and segmental-duplication content

0101010101010101

annotated_intervals 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.

Merge unmapped with mapped BAM files

0120101

bam 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.

Convert a mappability file to bedgraph format

0101

bedgraph sizes versions

gem2:

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:

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:

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

gem3:

The GEM indexer (v3).

Performs fastq alignment to a fasta reference using using gem3-mapper

01010

bam versions

gem3:

The GEM indexer (v3).

create index file for genmap

01

index versions

genmap:

Ultra-fast computation of genome mappability.

create mappability files for a genome

0101

wig bedgraph txt csv versions

genmap:

Ultra-fast computation of genome mappability.

Genotype Salmonella Typhi from Mykrobe results

01

tsv versions

genotyphi:

Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)

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

0101201

annotated_gtf combined_gtf tmap refmap loci stats tracking versions

A versatile pairwise aligner for genomic and spliced nucleotide sequences

0100

sam versions

graphmap2:

A versatile pairwise aligner for genomic and spliced nucleotide sequences.

A versatile pairwise aligner for genomic and spliced nucleotide sequences

0

index versions

graphmap2:

A versatile pairwise aligner for genomic and spliced nucleotide sequences.

run the Broad Gene Set Enrichment tool in GSEA mode

0123010

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

gsea:

Gene Set Enrichment Analysis (GSEA)

Align RNA-Seq reads to a reference with HISAT2

010101

bam summary fastq versions

hisat2:

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:

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:

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.

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

hlala:

HLA typing from short and long reads

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

hmmcopy:

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

hmmcopy:

C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy

count how many reads map to each feature

01201

txt versions

htseq/count:

HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.

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.

0101

output versions

ilastik:

Ilastik is a user friendly tool that enables pixel classification, segmentation and analysis.

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

instrain:

Calculation of strain-level metrics

Produces a Newick format phylogeny from a multiple sequence alignment using the maximum likelihood algorithm. Capable of bacterial genome size alignments.

012000000000000

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

Identify insertion sites positions in bacterial genomes

0123

results versions

Generate k-mers (sketches) from FASTA/Q sequences

01

outdir info versions

kmcp:

Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping

Construct KMCP database from k-mer files

01

kmcp log versions

kmcp:

Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping

Merge search results from multiple databases.

01

result versions

kmcp:

Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping

Generate taxonomic profile from search results

010

profile versions

kmcp:

Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping

Search sequences against database

010

result versions

kmcp:

Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping

Uses Liftoff to accurately map annotations in GFF or GTF between assemblies of the same, or closely-related species

01000

gff3 polished_gff3 unmapped_txt versions

mageck count for functional genomics, reads are usually mapped to a specific sgRNA

010

count norm versions

mageck:

MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), an algorithm to process, QC, analyze and visualize CRISPR screening 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.

000

index versions log

malt:

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

malt:

A tool for mapping metagenomic data

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

manta:

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

manta:

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.

012345601010

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

manta:

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

manta:

Structural variant and indel caller for mapped sequencing data

Create mapAD index for reference genome

01

index versions

mapad:

An aDNA aware short-read mapper

Map short-reads to an indexed reference genome

01010000000

bam versions

mapad:

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

Mashmap is an approximate long read or contig mapper based on Jaccard similarity

0101

paf versions

A reimplemenation of KatGC to work with FastK databases

012

filled_gc_plot_png filled_gc_plot_pdf line_gc_plot_png line_gc_plot_pdf stacked_gc_plot_png stacked_gc_plot_pdf versions

merquryfk:

FastK based version of Merqury

Strain-level metagenomic assignment

012340

wimp evidence_unknown_species reads2taxon em contig_coverage length_and_id krona versions

metamaps:

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:

MetaMaps is a tool for long-read metagenomic analysis

A versatile pairwise aligner for genomic and spliced nucleotide sequences

01010000

paf bam index versions

minimap2:

A versatile pairwise aligner for genomic and spliced nucleotide sequences.

Provides fasta index required by minimap2 alignment.

01

index versions

minimap2:

A versatile pairwise aligner for genomic and spliced nucleotide sequences.

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:

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:

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.

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

mitohifi.py:

A python workflow that assembles mitogenomes from Pacbio HiFi reads

Performs fastq alignment to a reference using NARFMAP

0101010

bam log versions

narfmap:

narfmap is a fork of the Dragen mapper/aligner Open Source Software.

Create DRAGEN hashtable for reference genome

01

hashmap versions

narfmap:

narfmap is a fork of the Dragen mapper/aligner Open Source Software.

Performs fastq alignment to a fasta reference using NextGenMap

010

bam versions

bwa:

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

Find and remove PCR/optical duplicates

01

pairs stat versions

pairtools:

CLI tools to process mapped Hi-C data

Flip pairs to get an upper-triangular matrix

010

flip versions

pairtools:

CLI tools to process mapped Hi-C data

Merge multiple pairs/pairsam files

01

pairs versions

pairtools:

CLI tools to process mapped Hi-C data

Find ligation junctions in .sam, make .pairs

010

pairsam stat versions

pairtools:

CLI tools to process mapped Hi-C data

Assign restriction fragments to pairs

010

restrict versions

pairtools:

CLI tools to process mapped Hi-C data

Select pairs according to given condition by options.args

01

selected unselected versions

pairtools:

CLI tools to process mapped Hi-C data

Sort a .pairs/.pairsam file

01

sorted versions

pairtools:

CLI tools to process mapped Hi-C data

Split a .pairsam file into .pairs and .sam.

01

pairs bam versions

pairtools:

CLI tools to process mapped Hi-C data

Calculate pairs statistics

01

stats versions

pairtools:

CLI tools to process mapped Hi-C data

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

0101010

bam bai qc_metrics bqsr_table duplicate_metrics versions

parabricks:

NVIDIA Clara Parabricks GPU-accelerated genomics tools

Alignment with PacBio's minimap2 frontend

0101

bam versions

pbmm2:

A minimap2 frontend for PacBio native data formats

Cleans the provided BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads

01

bam versions

picard:

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

Recodes plink bfiles into a new text fileset applying different modifiers

0123

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

plink:

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

converts sam/bam/cram/pairs into genome contact map

01012

pretext versions

a module to generate images from Pretext contact maps.

01

image versions

frame-shift correction for long read (meta)genomics - maps proteins to reads

012

tsv versions

proovframe:

frame-shift correction for long read (meta)genomics

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.

012300

rds png bias_rds bias_bed low_cov_bed versions

purecn:

Copy number calling and SNV classification using targeted short read sequencing

Evaluate alignment data

010

results versions

qualimap:

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

012000

results versions

qualimap:

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

0101

results versions

qualimap:

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.

Calculate how mapped reads are distributed over genomic features

010

txt versions

rseqc:

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:

RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data.

Calling lowest common ancestors from multi-mapped reads in SAM/BAM/CRAM files

0120

csv json bam versions

sam2lca:

Lowest Common Ancestor on SAM/BAM/CRAM alignment files

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 versions

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.

Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type

012

flagstat versions

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.

Reports alignment summary statistics for a BAM/CRAM/SAM file

012

idxstats versions

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.

converts FASTQ files to unmapped SAM/BAM/CRAM

01

sam bam cram versions

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.

SCIMAP is a suite of tools that enables spatial single-cell analyses

01

csv h5ad versions

scimap:

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:

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

scramble:

Soft Clipped Read Alignment Mapper

The cluster_identifier tool of Scramble identifies soft clipped clusters

0120

clusters versions

scramble:

Soft Clipped Read Alignment Mapper

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

0100

alignment trans_alignments multi_bed single_bed versions

segemehl:

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

Generate genome indices for segemehl align

0

index versions

segemehl:

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

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

sentieon:

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

sentieon:

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

sentieon:

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

sentieon:

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

sentieon:

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

sentieon:

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

sentieon:

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

sentieon:

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

sentieon:

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

sentieon:

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

sentieon:

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

sentieon:

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

sentieon:

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

sentieon:

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

sentieon:

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

sentieon:

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

sentieon:

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

sentieon:

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 SNAP

0101

bam bai versions

snapaligner:

Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data

Local sequence alignment tool for filtering, mapping and clustering.

010101

reads log index versions

SortMeRNA:

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.

Create a database of sourmash signatures (a group of FracMinHash sketches) to be used as references.

010

signature_index versions

sourmash:

Compute and compare FracMinHash signatures for DNA data sets.

Module to use the 10x Space Ranger pipeline to process 10x spatial transcriptomics data

0123456700

outs versions

spaceranger:

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

spaceranger:

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

spaceranger:

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.

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:

STAR is a software package for mapping DNA sequences against a large reference genome, such as the human genome.

Create index for STAR

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index versions

star:

STAR is a software package for mapping DNA sequences against a large reference genome, such as the human genome.

Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation

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vcf vcf_tbi genome_vcf genome_vcf_tbi versions

strelka:

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:

Strelka calls somatic and germline small variants from mapped sequencing reads

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.

uLTRA aligner - A wrapper around minimap2 to improve small exon detection - Map reads on genome

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bam versions

ultra:

Splice aligner of long transcriptomic reads to genome.

uLTRA aligner - A wrapper around minimap2 to improve small exon detection - Index gtf file for reads alignment

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index versions

ultra:

Splice aligner of long transcriptomic reads to genome.

uLTRA aligner - A wrapper around minimap2 to improve small exon detection

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sam versions

ultra:

Splice aligner of long transcriptomic reads to genome.

Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read.

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bam fastq log versions

Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read.

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bam log tsv_edit_distance tsv_per_umi tsv_umi_per_position versions

umi_tools:

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

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log bam tsv versions

umi_tools:

UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes

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

a pangenome-scale aligner

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paf versions

Align reads to a reference genome using YARA

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bam bai versions

yara:

Yara is an exact tool for aligning DNA sequencing reads to reference genomes.

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