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 148
  • fasta 141
  • vcf 105
  • fastq 96
  • metagenomics 65
  • index 64
  • gatk4 60
  • reference 60
  • genome 59
  • bed 55
  • genomics 55
  • alignment 51
  • cram 50
  • assembly 49
  • sam 46
  • sort 39
  • structural variants 34
  • annotation 31
  • variant calling 30
  • merge 30
  • align 30
  • database 30
  • bacteria 27
  • map 25
  • filter 24
  • statistics 24
  • coverage 22
  • gff 21
  • qc 20
  • classify 18
  • nanopore 18
  • quality control 18
  • gtf 18
  • cnv 18
  • gfa 18
  • download 17
  • variants 17
  • contamination 16
  • k-mer 16
  • taxonomic profiling 16
  • split 15
  • binning 15
  • classification 14
  • sentieon 14
  • ancient DNA 14
  • somatic 13
  • copy number 13
  • VCF 13
  • contigs 13
  • count 13
  • quality 13
  • gvcf 12
  • bisulfite 12
  • trimming 12
  • variation graph 12
  • variant 12
  • bedtools 12
  • taxonomy 12
  • databases 11
  • bisulphite 11
  • convert 11
  • methylseq 11
  • imputation 11
  • clustering 11
  • conversion 10
  • 5mC 10
  • serotype 10
  • consensus 10
  • graph 10
  • cna 10
  • picard 10
  • illumina 10
  • sequences 10
  • indexing 10
  • methylation 10
  • table 10
  • DNA methylation 9
  • aDNA 9
  • WGBS 9
  • bins 9
  • scWGBS 9
  • plot 9
  • protein sequence 9
  • MSA 9
  • bqsr 9
  • searching 9
  • metrics 9
  • pangenome graph 9
  • isoseq 9
  • haplotype 9
  • antimicrobial resistance 9
  • sv 9
  • histogram 9
  • visualisation 9
  • phage 9
  • reporting 8
  • iCLIP 8
  • expression 8
  • cooler 8
  • annotate 8
  • bcftools 8
  • depth 8
  • compression 8
  • phylogeny 8
  • proteomics 8
  • damage 8
  • wgs 8
  • checkm 8
  • low-coverage 8
  • archaeogenomics 8
  • stats 8
  • matrix 8
  • markduplicates 8
  • biscuit 8
  • protein 8
  • palaeogenomics 8
  • base quality score recalibration 8
  • bisulfite sequencing 8
  • rnaseq 8
  • LAST 8
  • demultiplex 8
  • tsv 8
  • mkref 7
  • mag 7
  • mags 7
  • metagenome 7
  • pacbio 7
  • completeness 7
  • virus 7
  • bismark 7
  • samtools 7
  • mappability 7
  • kmer 7
  • amr 7
  • mmseqs2 7
  • dedup 7
  • ucsc 7
  • peaks 7
  • phasing 7
  • pairs 7
  • aligner 7
  • newick 7
  • glimpse 7
  • repeat 6
  • bwa 6
  • bedGraph 6
  • prokaryote 6
  • filtering 6
  • germline 6
  • build 6
  • openms 6
  • decompression 6
  • NCBI 6
  • QC 6
  • tumor-only 6
  • genotype 6
  • mitochondria 6
  • single 6
  • kmers 6
  • cnvkit 6
  • ncbi 6
  • pangenome 6
  • validation 6
  • complexity 6
  • db 6
  • kallisto 5
  • MAF 5
  • umi 5
  • single-cell 5
  • mutect2 5
  • counts 5
  • interval 5
  • plasmid 5
  • structure 5
  • splicing 5
  • msa 5
  • 3-letter genome 5
  • de novo assembly 5
  • seqkit 5
  • isolates 5
  • extract 5
  • multiple sequence alignment 5
  • mapping 5
  • transcriptome 5
  • blast 5
  • report 5
  • sourmash 5
  • snp 5
  • svtk 5
  • de novo 5
  • deduplication 5
  • antimicrobial resistance genes 5
  • differential 5
  • transcript 5
  • feature 5
  • fragment 5
  • benchmark 5
  • adapters 5
  • json 5
  • imaging 5
  • view 5
  • microbiome 5
  • population genetics 5
  • prediction 5
  • antibiotic resistance 5
  • deamination 5
  • miscoding lesions 4
  • bedgraph 4
  • interval_list 4
  • haplotypecaller 4
  • indels 4
  • ancestry 4
  • segmentation 4
  • text 4
  • cluster 4
  • csv 4
  • genmod 4
  • idXML 4
  • concatenate 4
  • ranking 4
  • compress 4
  • biosynthetic gene cluster 4
  • hic 4
  • compare 4
  • mem 4
  • short-read 4
  • BGC 4
  • FASTQ 4
  • umitools 4
  • clipping 4
  • cut 4
  • public datasets 4
  • palaeogenetics 4
  • archaeogenetics 4
  • deep learning 4
  • cnv calling 4
  • arg 4
  • diamond 4
  • diversity 4
  • ATAC-seq 4
  • CLIP 4
  • merging 4
  • phylogenetic placement 4
  • profiling 4
  • circrna 4
  • STR 4
  • resistance 4
  • fgbio 4
  • long reads 4
  • genome assembler 4
  • vsearch 4
  • taxonomic classification 4
  • tabular 4
  • ganon 4
  • genotyping 4
  • fungi 4
  • DNA sequence 4
  • hmmcopy 4
  • low frequency variant calling 4
  • paf 4
  • DNA sequencing 4
  • targeted sequencing 4
  • hybrid capture sequencing 4
  • copy number alteration calling 4
  • malt 4
  • quantification 4
  • mpileup 4
  • ngscheckmate 4
  • matching 4
  • hmmsearch 4
  • retrotransposon 4
  • hmmer 4
  • containment 4
  • summary 4
  • duplicates 4
  • family 4
  • query 4
  • antimicrobial peptides 3
  • structural_variants 3
  • SV 3
  • typing 3
  • CRISPR 3
  • msi 3
  • entrez 3
  • sequencing 3
  • ataqv 3
  • sequence 3
  • rsem 3
  • detection 3
  • arriba 3
  • npz 3
  • windowmasker 3
  • evaluation 3
  • polishing 3
  • snps 3
  • pan-genome 3
  • gff3 3
  • pairsam 3
  • plink2 3
  • propr 3
  • das_tool 3
  • logratio 3
  • C to T 3
  • fam 3
  • deeparg 3
  • bim 3
  • neural network 3
  • das tool 3
  • gsea 3
  • prefetch 3
  • scores 3
  • fingerprint 3
  • PCA 3
  • profile 3
  • prokka 3
  • variant_calling 3
  • bacterial 3
  • genomes 3
  • bin 3
  • small indels 3
  • identity 3
  • amplicon sequencing 3
  • ccs 3
  • HMM 3
  • hidden Markov model 3
  • score 3
  • peak-calling 3
  • genome mining 3
  • informative sites 3
  • genome assembly 3
  • kinship 3
  • PacBio 3
  • notebook 3
  • relatedness 3
  • happy 3
  • bgzip 3
  • shapeit 3
  • ligate 3
  • gridss 3
  • enrichment 3
  • long-read 3
  • lossless 3
  • chimeras 3
  • survivor 3
  • reports 3
  • panel 3
  • microarray 3
  • vrhyme 3
  • observations 3
  • wxs 3
  • wastewater 3
  • virulence 3
  • indel 3
  • spark 3
  • archiving 3
  • zip 3
  • unzip 3
  • uncompress 3
  • krona chart 3
  • krona 3
  • ont 3
  • long_read 3
  • insert 3
  • minimap2 3
  • uLTRA 3
  • eukaryotes 3
  • bigwig 3
  • prokaryotes 3
  • pseudoalignment 3
  • tabix 3
  • spaceranger 3
  • fusion 3
  • dump 3
  • bcl2fastq 3
  • converter 3
  • bakta 3
  • host 3
  • png 3
  • wig 3
  • redundancy 3
  • organelle 3
  • gene 3
  • bamtools 3
  • checkv 3
  • microbes 3
  • kraken 3
  • gene expression 3
  • cellranger 3
  • mkfastq 3
  • roh 3
  • chromosome 3
  • bcf 3
  • comparisons 3
  • gzip 3
  • telomere 3
  • hi-c 3
  • aln 3
  • adapter trimming 3
  • quality trimming 3
  • kraken2 3
  • abundance 3
  • normalization 3
  • add 3
  • complement 3
  • gatk4spark 3
  • chunk 3
  • cool 3
  • cut up 3
  • salmonella 2
  • interval list 2
  • spatial 2
  • awk 2
  • runs_of_homozygosity 2
  • filtermutectcalls 2
  • blastn 2
  • union 2
  • trim 2
  • sra-tools 2
  • antismash 2
  • visualization 2
  • krakenuniq 2
  • soft-clipped clusters 2
  • untar 2
  • replace 2
  • interactive 2
  • rgfa 2
  • megan 2
  • dictionary 2
  • trancriptome 2
  • panelofnormals 2
  • vdj 2
  • settings 2
  • tama 2
  • angsd 2
  • shigella 2
  • html 2
  • deconvolution 2
  • retrotransposons 2
  • duplicate purging 2
  • subsample 2
  • ampir 2
  • transposons 2
  • SNP 2
  • serogroup 2
  • genome bins 2
  • mlst 2
  • bayesian 2
  • single cells 2
  • scatter 2
  • Duplication purging 2
  • vg 2
  • switch 2
  • khmer 2
  • image_analysis 2
  • pileup 2
  • Read depth 2
  • realignment 2
  • spatial_transcriptomics 2
  • resolve_bioscience 2
  • profiles 2
  • mzml 2
  • xz 2
  • gstama 2
  • COBS 2
  • nucleotide 2
  • join 2
  • secondary metabolites 2
  • concordance 2
  • de novo assembler 2
  • small genome 2
  • bwameth 2
  • RiPP 2
  • cat 2
  • gem 2
  • barcode 2
  • bam2fq 2
  • baf 2
  • signature 2
  • k-mer index 2
  • genomad 2
  • NRPS 2
  • function 2
  • FracMinHash sketch 2
  • lofreq 2
  • combine 2
  • bloom filter 2
  • ChIP-seq 2
  • pharokka 2
  • image 2
  • preprocessing 2
  • homoploymer,microsatellite 2
  • standardisation 2
  • junctions 2
  • checksum 2
  • reheader 2
  • pair 2
  • immunoprofiling 2
  • joint genotyping 2
  • gene set 2
  • taxon tables 2
  • otu tables 2
  • gene set analysis 2
  • rtgtools 2
  • antibiotics 2
  • cancer genomics 2
  • standardise 2
  • taxonomic profile 2
  • mash 2
  • cnvnator 2
  • ped 2
  • standardization 2
  • benchmarking 2
  • effect prediction 2
  • scaffolding 2
  • snpeff 2
  • snpsift 2
  • purge duplications 2
  • bustools 2
  • fasterq-dump 2
  • long terminal retrotransposon 2
  • intersect 2
  • cfDNA 2
  • ichorcna 2
  • estimation 2
  • sequenzautils 2
  • HOPS 2
  • eido 2
  • import 2
  • format 2
  • authentication 2
  • guide tree 2
  • MaltExtract 2
  • blastp 2
  • eigenstrat 2
  • adapter 2
  • tbi 2
  • preseq 2
  • graph layout 2
  • merge mate pairs 2
  • library 2
  • fusions 2
  • recombination 2
  • mask 2
  • emboss 2
  • variant pruning 2
  • cvnkit 2
  • SimpleAF 2
  • varcal 2
  • maximum likelihood 2
  • iphop 2
  • gwas 2
  • tnhaplotyper2 2
  • GPU-accelerated 2
  • instrain 2
  • read depth 2
  • metagenomes 2
  • random forest 2
  • sample 2
  • somatic variants 2
  • transformation 2
  • deseq2 2
  • regions 2
  • mitochondrion 2
  • heatmap 2
  • intervals 2
  • orthology 2
  • parallelized 2
  • normalize 2
  • amps 2
  • structural 2
  • norm 2
  • rna-seq 2
  • demultiplexed reads 2
  • mtDNA 2
  • concat 2
  • intersection 2
  • hla_typing 2
  • sketch 2
  • hlala 2
  • unaligned 2
  • ancient dna 2
  • windows 2
  • metagenomic 2
  • fai 2
  • scRNA-seq 2
  • proportionality 2
  • nextclade 2
  • fastk 2
  • reads 2
  • hla 2
  • highly_multiplexed_imaging 2
  • edit distance 2
  • HiFi 2
  • long terminal repeat 2
  • atac-seq 2
  • salmon 2
  • hlala_typing 2
  • chip-seq 2
  • expansionhunterdenovo 2
  • artic 2
  • Streptococcus pneumoniae 2
  • transcriptomic 2
  • eCLIP 2
  • mapcounter 2
  • reads merging 2
  • short reads 2
  • tab 2
  • mudskipper 2
  • mcmicro 2
  • repeat_expansions 2
  • aggregate 2
  • comparison 2
  • metadata 2
  • micro-satellite-scan 2
  • msisensor-pro 2
  • simulate 2
  • UMI 2
  • parse 2
  • RNA-Seq 2
  • structural-variant calling 2
  • plastid 1
  • chromatin 1
  • VQSR 1
  • applyvarcal 1
  • pcr 1
  • variant recalibration 1
  • cut&tag 1
  • affy 1
  • read pairs 1
  • seacr 1
  • readgroup 1
  • rna 1
  • nucleotide sequence 1
  • kma 1
  • resfinder 1
  • mate-pair 1
  • single cell 1
  • paired 1
  • faidx 1
  • scramble 1
  • repair 1
  • peak-caller 1
  • insert size 1
  • cut&run 1
  • liftovervcf 1
  • assembly-binning 1
  • fixmate 1
  • dict 1
  • NETCAGE 1
  • collate 1
  • CoPRO 1
  • coexpression 1
  • r 1
  • contact 1
  • pretext 1
  • jpg 1
  • bmp 1
  • contact maps 1
  • gene finding 1
  • microbial 1
  • intervals coverage 1
  • demultiplexing 1
  • python 1
  • quarto 1
  • genomic intervals 1
  • normal database 1
  • panel of normals 1
  • cutoff 1
  • haplotype purging 1
  • false duplications 1
  • assembly curation 1
  • Haplotype purging 1
  • correlation 1
  • porechop_abi 1
  • Assembly curation 1
  • dna sequencing 1
  • CAGE 1
  • RAMPAGE 1
  • csRNA-seq 1
  • minimum_evolution 1
  • STRIPE-seq 1
  • PRO-seq 1
  • PRO-cap 1
  • GRO-seq 1
  • phylogenetics 1
  • GRO-cap 1
  • pmdtools 1
  • parsing 1
  • assay 1
  • exclude 1
  • indep 1
  • indep pairwise 1
  • recode 1
  • corpcor 1
  • identifiers 1
  • scoring 1
  • variant genetic 1
  • False duplications 1
  • standardize 1
  • picard/renamesampleinvcf 1
  • salsa2 1
  • rtg 1
  • pedfilter 1
  • insertions 1
  • rocplot 1
  • rtg-tools 1
  • salsa 1
  • raw 1
  • resistance genes 1
  • distance-based 1
  • LCA 1
  • Staphylococcus aureus 1
  • Ancestor 1
  • multimapper 1
  • flagstat 1
  • sambamba 1
  • duplicate marking 1
  • amplicon 1
  • ampliconclip 1
  • deletions 1
  • calmd 1
  • sortvcf 1
  • integrity 1
  • mapping-based 1
  • split assembly 1
  • parser 1
  • dbsnp 1
  • quast 1
  • contig 1
  • scaffold 1
  • polish 1
  • neighbour-joining 1
  • subsampling 1
  • long uncorrected reads 1
  • rhocall 1
  • R 1
  • parquet 1
  • sequence-based 1
  • bamstat 1
  • allele 1
  • strandedness 1
  • experiment 1
  • read_pairs 1
  • mgf 1
  • tandem duplications 1
  • inner_distance 1
  • read distribution 1
  • duplication 1
  • fragment_size 1
  • predictions 1
  • subseq 1
  • copy number variation 1
  • mashmap 1
  • wavefront 1
  • structural variant 1
  • whamg 1
  • wham 1
  • copy-number 1
  • copy number analysis 1
  • gender determination 1
  • copy number alterations 1
  • yahs 1
  • pangenome-scale 1
  • geo 1
  • mapad 1
  • adna 1
  • rad 1
  • c to t 1
  • mapper 1
  • proteus 1
  • readproteingroups 1
  • calling 1
  • eigenvectors 1
  • all versus all 1
  • long read alignment 1
  • sliding 1
  • deduplicate 1
  • vcf2db 1
  • gemini 1
  • immunoinformatics 1
  • maf 1
  • lua 1
  • toml 1
  • vcflib 1
  • vcflib/vcfbreakmulti 1
  • airrseq 1
  • uniq 1
  • VCFtools 1
  • usearch 1
  • construct 1
  • graph projection to vcf 1
  • immcantation 1
  • bam2fastq 1
  • extractunbinned 1
  • linkbins 1
  • bam2fastx 1
  • sintax 1
  • vsearch/sort 1
  • amplicon sequences 1
  • hicPCA 1
  • gost 1
  • downsample bam 1
  • nucleotides 1
  • ancestral alleles 1
  • boxcox 1
  • site frequency spectrum 1
  • Escherichia coli 1
  • peak picking 1
  • reformatting 1
  • sompy 1
  • Read coverage histogram 1
  • removal 1
  • reverse complement 1
  • derived alleles 1
  • simulation 1
  • rrna 1
  • htseq 1
  • hmmfetch 1
  • decompose 1
  • multiallelic 1
  • small variants 1
  • transmembrane 1
  • genome graph 1
  • tnseq 1
  • clr 1
  • alr 1
  • gprofiler2 1
  • antimicrobial reistance 1
  • vector 1
  • snakemake 1
  • workflow 1
  • workflow_mode 1
  • createreadcountpanelofnormals 1
  • copyratios 1
  • denoisereadcounts 1
  • readwriter 1
  • dnamodelapply 1
  • dnascope 1
  • cytosure 1
  • tnfilter 1
  • image_processing 1
  • registration 1
  • array_cgh 1
  • groupby 1
  • tnscope 1
  • bgen 1
  • chloroplast 1
  • confidence 1
  • blat 1
  • bedpe 1
  • subsample bam 1
  • downsample 1
  • grep 1
  • core 1
  • boxplot 1
  • density 1
  • features 1
  • genotypegvcf 1
  • sliding window 1
  • joint-genotyping 1
  • copy number, BAM, CRAM, SMN1, SMN2 1
  • POA 1
  • sniffles 1
  • snippy 1
  • shinyngs 1
  • install 1
  • snp-dists 1
  • distance-matrix 1
  • dbnsfp 1
  • decoy 1
  • SNPs 1
  • invariant 1
  • constant 1
  • introns 1
  • gaps 1
  • exploratory 1
  • contiguate 1
  • rRNA 1
  • bam2seqz 1
  • sertotype 1
  • seqtk 1
  • interleave 1
  • rename 1
  • seq 1
  • filtering,selection 1
  • random draw 1
  • pseudohaploid 1
  • pseudodiploid 1
  • freqsum 1
  • gc_wiggle 1
  • 256 bit 1
  • induce 1
  • parallel 1
  • sex determination 1
  • genetic sex 1
  • relative coverage 1
  • rare variants 1
  • error 1
  • de-novo 1
  • longread 1
  • sha256 1
  • transform 1
  • ribosomal RNA 1
  • snv 1
  • ucsc/liftover 1
  • eucaryotes 1
  • sequencing adapters 1
  • adapterremoval 1
  • bedgraphtobigwig 1
  • bigbed 1
  • bedtobigbed 1
  • genepred 1
  • refflat 1
  • gtftogenepred 1
  • comparative genomics 1
  • Mycobacterium tuberculosis 1
  • spectral clustering 1
  • sequence similarity 1
  • umicollapse 1
  • homology 1
  • scRNA-Seq 1
  • co-orthology 1
  • files 1
  • upd 1
  • uniparental 1
  • disomy 1
  • chromosomal rearrangements 1
  • archive 1
  • reference panels 1
  • short-read sequencing 1
  • signatures 1
  • hash sketch 1
  • fracminhash sketch 1
  • idx 1
  • spatype 1
  • streptococcus 1
  • sccmec 1
  • variantcalling 1
  • admixture 1
  • detecting svs 1
  • svdb 1
  • deep variant 1
  • mutect 1
  • svtk/baftest 1
  • baftest 1
  • countsvtypes 1
  • rdtest2vcf 1
  • rdtest 1
  • vcf2bed 1
  • decompress 1
  • polya tail 1
  • fast5 1
  • hybrid-selection 1
  • AMP 1
  • clean 1
  • duplexumi 1
  • identifier 1
  • ANI 1
  • SRA 1
  • ENA 1
  • GEO 1
  • fetch 1
  • public 1
  • autozygosity 1
  • duplex 1
  • UMIs 1
  • consensus sequence 1
  • groupreads 1
  • antibiotic resistance genes 1
  • zipperbams 1
  • http(s) 1
  • single molecule 1
  • generate 1
  • lint 1
  • fq 1
  • rust 1
  • variant caller 1
  • somatic variant calling 1
  • germline variant calling 1
  • bacterial variant calling 1
  • bootstrapping 1
  • ARGs 1
  • faqcs 1
  • gamma 1
  • schema 1
  • cumulative coverage 1
  • machine learning 1
  • post mortem damage 1
  • blastx 1
  • segment 1
  • atlas 1
  • escherichia coli 1
  • mkarv 1
  • PEP 1
  • samplesheet 1
  • validate 1
  • pep 1
  • str 1
  • eigenstratdatabasetools 1
  • eklipse 1
  • circos 1
  • deletion 1
  • split by chromosome 1
  • embl 1
  • genbank 1
  • swissprot 1
  • Streptococcus pyogenes 1
  • endogenous DNA 1
  • percent on target 1
  • cache 1
  • UShER 1
  • gene-calling 1
  • scatterplot 1
  • germlinevariantsites 1
  • filterintervals 1
  • filtervarianttranches 1
  • tranche filtering 1
  • gatherbqsrreports 1
  • genomicsdb 1
  • genomicsdbimport 1
  • jointgenotyping 1
  • panelofnormalscreation 1
  • gatk 1
  • germline contig ploidy 1
  • germlinecnvcaller 1
  • getpileupsumaries 1
  • duplication metrics 1
  • readcountssummary 1
  • indexfeaturefile 1
  • learnreadorientationmodel 1
  • readorientationartifacts 1
  • leftalignandtrimvariants 1
  • mergebamalignment 1
  • mutectstats 1
  • snvs 1
  • postprocessgermlinecnvcalls 1
  • preprocessintervals 1
  • printreads 1
  • printsvevidence 1
  • estimatelibrarycomplexity 1
  • determinegermlinecontigploidy 1
  • gangstr 1
  • calculatecontamination 1
  • heattree 1
  • targets 1
  • annotateintervals 1
  • utility 1
  • RNA-seq 1
  • HLA 1
  • variant quality score recalibration 1
  • vqsr 1
  • allele-specific 1
  • asereadcounter 1
  • bedtointervallist 1
  • cross-samplecontamination 1
  • createsomaticpanelofnormals 1
  • getpileupsummaries 1
  • calibratedragstrmodel 1
  • cnnscorevariants 1
  • collectreadcounts 1
  • collectsvevidence 1
  • combinegvcfs 1
  • short variant discovery 1
  • composestrtablefile 1
  • dragstr 1
  • condensedepthevidence 1
  • evidence 1
  • createsequencedictionary 1
  • sequencing_bias 1
  • corrrelation 1
  • revert 1
  • hifi 1
  • clumping fastqs 1
  • tblastn 1
  • bracken 1
  • proteome 1
  • cadd 1
  • calder2 1
  • topology 1
  • compartments 1
  • domains 1
  • Assembly 1
  • microscopy 1
  • background_correction 1
  • deduping 1
  • illumiation_correction 1
  • cellpose 1
  • element 1
  • mkvdjref 1
  • trimBam 1
  • multiomics 1
  • antigen capture 1
  • antibody capture 1
  • crispr 1
  • bamUtil 1
  • bamtools/split 1
  • yaml 1
  • smaller fastqs 1
  • remove 1
  • qa 1
  • overlapped bed 1
  • homozygosity 1
  • biallelic 1
  • bamtobed 1
  • closest 1
  • update header 1
  • genomecov 1
  • getfasta 1
  • overlap 1
  • jaccard 1
  • chunking 1
  • maskfasta 1
  • multinterval 1
  • BAM 1
  • shiftBed 1
  • region 1
  • sizes 1
  • bases 1
  • slopBed 1
  • subtract 1
  • unionBedGraphs 1
  • bioawk 1
  • file manipulation 1
  • Salmonella enterica 1
  • subtyping 1
  • csi 1
  • bamtools/convert 1
  • quality assurnce 1
  • track 1
  • version 1
  • enzyme 1
  • makebins 1
  • genomic bins 1
  • mcool 1
  • UNet 1
  • TMA dearray 1
  • Segmentation 1
  • Cores 1
  • CNV 1
  • correction 1
  • custom 1
  • background 1
  • cload 1
  • na 1
  • cls 1
  • gct 1
  • cutesv 1
  • single-stranded 1
  • ancientDNA 1
  • authentict 1
  • pcr duplicates 1
  • paired-end 1
  • read group 1
  • spatial_omics 1
  • ATLAS 1
  • digest 1
  • cycif 1
  • chromap 1
  • antitarget 1
  • duplicate removal 1
  • chromosome_visualization 1
  • splice 1
  • mouse 1
  • graft 1
  • polymut 1
  • polymorphic 1
  • polymorphic sites 1
  • protein coding genes 1
  • cmseq 1
  • access 1
  • xenograft 1
  • cooler/balance 1
  • export 1
  • target 1
  • CNV calling 1
  • partition histograms 1
  • bacphlip 1
  • virulent 1
  • temperate 1
  • concoct 1
  • lifestyle 1
  • nucleotide composition 1
  • subcontigs 1
  • autofluorescence 1
  • reblockgvcf 1
  • selectvariants 1
  • macrel 1
  • metaphlan 1
  • Neisseria meningitidis 1
  • k-mer frequency 1
  • GC content 1
  • 3D heat map 1
  • contour map 1
  • Merqury 1
  • reference-free 1
  • assembly evaluation 1
  • smudgeplot 1
  • ploidy 1
  • unionsum 1
  • methylation bias 1
  • daa 1
  • mbias 1
  • microrna 1
  • mirna 1
  • target prediction 1
  • mitochondrial genome 1
  • reference genome 1
  • amp 1
  • DRAMP 1
  • neubi 1
  • mosdepth 1
  • otu table 1
  • scan 1
  • rma6 1
  • debruijn 1
  • ratio 1
  • mash/dist 1
  • sorting 1
  • peptide prediction 1
  • AMPs 1
  • functional genomics 1
  • sgRNA 1
  • CRISPR-Cas9 1
  • maximum-likelihood 1
  • rra 1
  • DNA damage 1
  • NGS 1
  • damage patterns 1
  • screen 1
  • denovo 1
  • taxonomic assignment 1
  • mash/sketch 1
  • minhash 1
  • reduced 1
  • representations 1
  • tree 1
  • maxbin2 1
  • antimicrobial peptide prediction 1
  • metagenome-assembled genomes 1
  • MD5 1
  • 128 bit 1
  • megahit 1
  • mtnucratio 1
  • mitochondrial to nuclear ratio 1
  • lofreq/filter 1
  • pbbam/pbmerge 1
  • ligation junctions 1
  • pairtools 1
  • pairstools 1
  • restriction fragments 1
  • select 1
  • covid 1
  • pangolin 1
  • lineage 1
  • paragraph 1
  • graphs 1
  • pbbam 1
  • subreads 1
  • flip 1
  • pbp 1
  • pair-end 1
  • read 1
  • pedigrees 1
  • motif 1
  • ChIP-Seq 1
  • phantom peaks 1
  • prophage 1
  • identification 1
  • illumina datasets 1
  • phylogenetic composition 1
  • read-group 1
  • upper-triangular matrix 1
  • amplify 1
  • bioinformatics tools 1
  • gender 1
  • Beautiful stand-alone HTML report 1
  • GATK UnifiedGenotyper 1
  • SNP table 1
  • contaminant_removal 1
  • cancer genome 1
  • somatic structural variations 1
  • mobile element insertions 1
  • sequencing summary 1
  • NextGenMap 1
  • ngm 1
  • Neisseria gonorrhoeae 1
  • graph construction 1
  • PCR/optical duplicates 1
  • graph drawing 1
  • squeeze 1
  • odgi 1
  • combine graphs 1
  • graph stats 1
  • graph unchopping 1
  • graph formats 1
  • graph viz 1
  • tumor/normal 1
  • hla-typing 1
  • ILP 1
  • HLA-I 1
  • qualities 1
  • call 1
  • shiftchain 1
  • TAMA 1
  • phase 1
  • Sample 1
  • Haplotypes 1
  • Imputation 1
  • GNU 1
  • merge compare 1
  • genomes on a tree 1
  • doCounts 1
  • tama_collapse.py 1
  • allele counts 1
  • gene model 1
  • gstama/merge 1
  • low coverage 1
  • gstama/polyacleanup 1
  • GTDB taxonomy 1
  • genome taxonomy database 1
  • archaea 1
  • gunc 1
  • gunzip 1
  • nuclear contamination estimate 1
  • gvcftools 1
  • extract_variants 1
  • extractvariants 1
  • abricate 1
  • amrfinderplus 1
  • installation 1
  • gget 1
  • rgi 1
  • txt 1
  • shiftfasta 1
  • shiftintervals 1
  • site depth 1
  • splitcram 1
  • splitintervals 1
  • svannotate 1
  • svcluster 1
  • variantfiltration 1
  • recalibration model 1
  • variantrecalibrator 1
  • gawk 1
  • file parsing 1
  • transcripts 1
  • bgc 1
  • genome profile 1
  • compound 1
  • models 1
  • genome size 1
  • genome heterozygosity 1
  • repeat content 1
  • Salmonella Typhi 1
  • gfastats 1
  • genome summary 1
  • genome manipulation 1
  • genome statistics 1
  • fARGene 1
  • ibd 1
  • lofreq/call 1
  • kegg 1
  • jasmine 1
  • Python 1
  • Jupyter 1
  • jupytext 1
  • papermill 1
  • kallisto/index 1
  • quant 1
  • digital normalization 1
  • effective genome size 1
  • screening assemblies 1
  • Klebsiella pneumoniae 1
  • kofamscan 1
  • polyA_tail 1
  • krakentools 1
  • combining 1
  • model 1
  • reorder 1
  • spliced 1
  • train 1
  • adapter removal 1
  • collapsing 1
  • legionella 1
  • primer 1
  • limma 1
  • Listeria monocytogenes 1
  • jasminesv 1
  • refine 1
  • hbd 1
  • haemophilus 1
  • beagle 1
  • mitochondrial 1
  • haplogroups. 1
  • post Post-processing 1
  • Haemophilus influenzae 1
  • haplotype resolution 1
  • gccounter 1
  • readcounter 1
  • hmtnote 1
  • annotations 1
  • pos 1
  • panel_of_normals 1
  • insertion sequences 1
  • IDR 1
  • igv 1
  • igv.js 1
  • js 1
  • genome browser 1
  • multicut 1
  • pixel classification 1
  • pixel_classification 1
  • probability_maps 1
  • population genomics 1
  • interproscan 1
  • genomic islands 1
  • homologs 1

contiguate draft genome assembly

metascaffoldfasta

meta results versions

Screen assemblies for antimicrobial resistance against multiple databases

metaassembly

meta versions report

abricate:

Mass screening of contigs for antibiotic resistance genes

Screen assemblies for antimicrobial resistance against multiple databases

metaassembly

meta versions summary

abricate:

Mass screening of contigs for antibiotic resistance genes

A NATA accredited tool for reporting the presence of antimicrobial resistance genes in bacterial genomes

metafasta

versions matches partials virulence txt out

abritamr:

A pipeline for running AMRfinderPlus and collating results into functional classes

Trim sequencing adapters and collapse overlapping reads

metareadsadapterlist

singles_truncated discarded paired_truncated collapsed collapsed_truncated paired_interleaved settings versions

Fixes prefixes from AdapterRemoval2 output to make sure no clashing read names are in the output. For use with DeDup.

metafastq

meta versions fixed_fastq

ADMIXTURE is a program for estimating ancestry in a model-based manner from large autosomal SNP genotype datasets, where the individuals are unrelated (for example, the individuals in a case-control association study).

metabed_ped_genobim_mapfamK

meta versions Q-ancestry-fractions P-allele-frequencies

Read CEL files into an ExpressionSet and generate a matrix

metasamplesheetcelfiles_dirdescription

meta expression annotation rds versions

affy:

Methods for Affymetrix Oligonucleotide Arrays

Converts a GFF/GTF file into a proper GTF file

metagff

output_gtf log versions

agat:

AGAT is a toolkit for manipulation and getting information from GFF/GTF files

Converts a GFF/GTF file into a TSV file

metagff

tsv versions

agat:

AGAT is a toolkit for manipulation and getting information from GFF/GTF files

Fixes and standardizes GFF/GTF files and outputs a cleaned GFF/GTF file

metagff

output_gff log versions

agat:

AGAT is a toolkit for manipulation and getting information from GFF/GTF files

Add intron features to gtf/gff file without intron features.

metagffconfig

versions gff

agat:

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

Provides different type of statistics in text format from a GFF/GTF annotation file

metagff

stats_txt versions

agat:

AGAT is a toolkit for manipulation and getting information from GFF/GTF files

Provides basic statistics in text format from a GFF/GTF annotation file

metagff

stats_txt versions

agat:

AGAT is a toolkit for manipulation and getting information from GFF/GTF files

Rapid identification of Staphylococcus aureus agr locus type and agr operon variants

metafasta

meta summary results_dir versions

Generates a count of coverage of alleles

metainputinput_indexlocifasta

meta versions allelecount

A tool to parse and summarise results from antimicrobial peptides tools and present functional classification.

metaamp_inputfaa_inputamp_database

meta versions txt csv faa log sample_dir results_db results_db_fasta results_db_dmd results_db_tsv summary_csv summary_html

A fast and user-friendly method to predict antimicrobial peptides (AMPs) from any given size protein dataset. ampir uses a supervised statistical machine learning approach to predict AMPs.

metafaamodelmin_lengthmin_probability

meta versions amps_faa amps_tsv

AMPlify is an attentive deep learning model for antimicrobial peptide prediction.

metafaamodel_dir

meta versions tsv

amplify:

Attentive deep learning model for antimicrobial peptide prediction

Post-processing script of the MaltExtract component of the HOPS package

maltextract_resultstaxon_listfilter

versions json summary_pdf tsv candidate_pdfs

Identify antimicrobial resistance in gene or protein sequences

metafastadb

meta versions report mutation_report tool_version db_version

amrfinderplus:

AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences.

Identify antimicrobial resistance in gene or protein sequences

NO input

meta versions db

amrfinderplus:

AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences.

A tool to estimate nuclear contamination in males based on heterozygosity in the female chromosome.

metaicountshapmap_file

meta versions txt

angsd:

ANGSD: Analysis of next generation Sequencing Data

Calculates base frequency statistics across reference positions from BAM.

metabambaiminqfile

meta versions depth_sample depth_global qs pos counts icounts

angsd:

ANGSD: Analysis of next generation Sequencing Data

Annotation and Ranking of Structural Variation

metasv_vcfsv_vcf_indexcandidate_small_variantsmeta2annotationsmeta3candidate_genesmeta4false_positive_snvmeta5gene_transcripts

meta versions tsv unannotated_tsv vcf

annotsv:

Annotation and Ranking of Structural Variation

Install the AnnotSV annotations

NO input

versions annotations

annotsv:

Annotation and Ranking of Structural Variation

antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters.

metasequence_inputdatabasesantismash_dirgff

meta versions clusterblast_file html_accessory_files knownclusterblast_html knownclusterblast_dir knownclusterblast_txt svg_files_clusterblast svg_files_knownclusterblast gbk_input json_results log zip gbk_results clusterblastoutput html knownclusterblastoutput json_sideloading

antismashlite:

antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell

antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. This module downloads the antiSMASH databases for conda and docker/singularity runs.

database_cssdatabase_detectiondatabase_modules

versions database antismash_dir

antismash:

antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell

Extracts reads mapped to chromosome 6 and any HLA decoys or chromosome 6 alternates.

metabam

meta 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.

CLI Download utility

metasource_url

meta downloaded_file versions

Download and prepare database for Ariba analysis

db_name

versions db

ariba:

ARIBA: Antibiotic Resistance Identification By Assembly

Query input FASTQs against Ariba formatted databases

metareadsdb

versions results

ariba:

ARIBA: Antibiotic Resistance Identification By Assembly

Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data.

metabammeta2fastameta3gtfmeta4blacklistmeta5known_fusionsmeta6structural_variantsmeta7tagsmeta8protein_domains

meta versions fusions fusions_fail

Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data.

metabammeta2fastameta3gtfmeta4blacklistmeta5known_fusionsmeta6structural_variantsmeta7tagsmeta8protein_domains

meta versions fusions fusions_fail

arriba:

Fast and accurate gene fusion detection from RNA-Seq data

Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data.

NO input

versions reference

arriba:

Fast and accurate gene fusion detection from RNA-Seq data

Simulation tool to generate synthetic Illumina next-generation sequencing reads

metafastasequencing_systemfold_coverageread_length

versions meta fastq aln sam

art:

ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles.

Aggregates fastq files with demultiplexed reads

metafastq_dir

meta fastq versions

artic:

ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore

Run the alignment/variant-call/consensus logic of the artic pipeline

metafastqfast5_dirsequencing_summaryprimer_scheme_fastaprimer_scheme_bedmedaka_model_filemedaka_model_stringschemescheme_version

meta results bam bai bam_trimmed bai_trimmed bam_primertrimmed bai_primertrimmed fasta vcf tbi json versions

artic:

ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore

copy number profiles of tumour cells.

argsmetainput_normalindex_normalinput_tumorindex_tumorallele_filesloci_filesbed_filefastagc_filert_file

meta allelefreqs metrics png purityploidy segments versions

Alignment by Simultaneous Harmonization of Layer/Adjacency Registration

metaimages

meta tif versions

Assembly summary statistics in JSON format

metaassembly

meta versions json

ataqv function of a corresponding ataqv tool

metabambaipeak_fileorganismmito_nametss_fileexcl_regs_fileautosom_ref_file

meta json problems versions

ataqv:

ataqv is a toolkit for measuring and comparing ATAC-seq results. It was written to help understand how well ATAC-seq assays have worked, and to make it easier to spot differences that might be caused by library prep or sequencing.

mkarv function of a corresponding ataqv tool

json

versions html

ataqv:

ataqv is a toolkit for measuring and comparing ATAC-seq results. It was written to help understand how well ATAC-seq assays have worked, and to make it easier to spot differences that might be caused by library prep or sequencing.

generate VCF file from a BAM file using various calling methods

metabambaifastafairecalpmdknown_allelesmethod

meta versions bam

atlas:

ATLAS, a suite of methods to accurately genotype and estimate genetic diversity

Estimate the post-mortem damage patterns of DNA

metabambaifastafaipool_rg_txt

meta versions empiric exponential counts table

atlas:

ATLAS, a suite of methods to accurately genotype and estimate genetic diversity

gives an estimation of the sequencing bias based on known invariant sites

metabambaiempiricallelesinvariant_sites

meta versions recal_patterns

atlas:

ATLAS, a suite of methods to accurately genotype and estimate genetic diversity

split single end read groups by length and merge paired end reads

metabambairead_group_settingblacklist

meta versions bam filelist

atlas:

ATLAS, a suite of methods to accurately genotype and estimate genetic diversity

Generate tables of feature metadata from GTF files

metameta2gtffasta

versions feature_annotation filtered_cdna

atlasgeneannotationmanipulation:

Scripts for manipulating gene annotation

Use deamination patterns to estimate contamination in single-stranded libraries

metabamconfigpositions

meta versions txt

authentict:

Estimates present-day DNA contamination in ancient DNA single-stranded libraries.

Pixel-by-pixel channel subtraction scaled by exposure times of pre-stitched tif images.

metaimagemeta2markerfile

meta versions backsub_tif meta2 markerout

A bacteriophage lifestyle prediction tool

metafasta

meta versions bacphlip_results hmmsearch_results

Annotation of bacterial genomes (isolates, MAGs) and plasmids

metafastadbproteinsprodigal_tf

meta versions txt tsv gff gbff embl fna faa ffn hypotheticals_tsv hypotheticals_faa

bakta:

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids.

Downloads BAKTA database from Zenodo

NO input

versions db

bakta:

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

Conversion of PacBio BAM files into gzipped fastq files, including splitting of barcoded data

metabamindex

meta versions fastq

bam2fastx:

Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files

bam

removes unused references from header of sorted BAM/CRAM files.

metabam

meta versions bam

Bamcmp (Bam Compare) is a tool for assigning reads between a primary genome and a contamination genome. For instance, filtering out mouse reads from patient derived xenograft mouse models (PDX).

metasamplecontaminant

versions bam bam

BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.

metabam

meta versions out

bamtools:

C++ API & command-line toolkit for working with BAM data

BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.

metabam

meta versions bam

bamtools:

C++ API & command-line toolkit for working with BAM data

BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.

metabam

meta versions stats

bamtools:

C++ API & command-line toolkit for working with BAM data

trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’, or by soft clipping

metabamtrim_lefttrim_right

meta versions bam

bamutil:

Programs that perform operations on SAM/BAM files, all built into a single executable, bam.

Render an assembly graph in GFA 1.0 format to PNG and SVG image formats

metagfa

meta png svg versions

bandage:

Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily

barrnap uses a hmmer profile to find rrnas in reads or contig fasta files

metareads

meta versions gff

Demultiplex Element Biosciences bases files

metarun_manifestrun_dir

meta versions sample_fastq sample_json qc_report run_stats generated_run_manifest metrics unassigned

BaSiCPy is a python package for background and shading correction of optical microscopy images. It is developed based on the Matlab version of BaSiC tool with major improvements in the algorithm.

metaimage

meta versions fields

Align short or PacBio reads to a reference genome using BBMap

metafastqref

meta versions bam

bbmap:

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

Adapter and quality trimming of sequencing reads

metareadscontaminants

meta reads 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.

metafastq

meta versions fastq

bbmap:

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

Split sequencing reads by mapping them to multiple references simultaneously

metareadsindexprimary_refother_ref_namesother_ref_pathsonly_build_index

meta versions index primary_fastq all_fastq stats

bbmap:

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

Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates

metareads

meta reads versions log

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.

fasta

versions db

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.

metabam

meta stats hist versions

bbmap:

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

Compares query sketches to reference sketches hosted on a remote server via the Internet.

metafile

meta versions hits

bbmap:

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

Add or remove annotations.

metainputindexannotationsannotations_indexheader_lines

meta versions vcf

annotate:

Add or remove annotations.

This command replaces the former bcftools view caller. Some of the original functionality has been temporarily lost in the process of transition under htslib, but will be added back on popular demand. The original calling model can be invoked with the -c option.

metavcfindexregionstargetssamples

meta vcf versions

view:

View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF

Concatenate VCF files

metavcfstbi

meta vcf versions

concat:

Concatenate VCF files.

Compresses VCF files

metavcftbifasta

meta fasta versions

consensus:

Create consensus sequence by applying VCF variants to a reference fasta file.

Converts certain output formats to VCF

metainputinput_indexmeta2fastabed

meta versions vcf_gz vcf bcf_gz bcf hap legend sample

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.

Filters VCF files

metavcf

meta vcf versions

filter:

Apply fixed-threshold filters to VCF files.

Index VCF tools

metaVCF

meta version csi tbi

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.

Apply set operations to VCF files

metavcfstbis

meta results versions

isec:

Computes intersections, unions and complements of VCF files.

Merge VCF files

metavcfstbismeta2fastameta3faibed

meta vcf_gz vcf bcf_gz bcf versions

merge:

Merge VCF files.

Compresses VCF files

metabamintervalsmetafastasave_mpileup

meta vcf tbi stats mpileup versions

mpileup:

Generates genotype likelihoods at each genomic position with coverage.

Normalize VCF file

metavcftbimeta2fasta

meta vcf versions

norm:

Normalize VCF files.

Split VCF by chunks or regions, creating multiple VCFs.

metavcftbisites_per_chunkscatterscatter_fileregionstargets

meta versions scatter

pluginscatter:

Split VCF by chunks or regions, creating multiple VCFs.

Split VCF by sample, creating single- or multi-sample VCFs.

metavcftbisamplesgroupsregionstargets

meta versions vcf

pluginsplit:

Split VCF by sample, creating single- or multi-sample VCFs.

Extracts fields from VCF or BCF files and outputs them in user-defined format.

metavcftbiregionstargetssamples

meta output versions

query:

Extracts fields from VCF or BCF files and outputs them in user-defined format.

Reheader a VCF file

metavcfheadersamplesmeta2fai

meta versions vcf

reheader:

Modify header of VCF/BCF files, change sample names.

A program for detecting runs of homo/autozygosity. Only bi-allelic sites are considered.

metavcfaf_fileaf_file_tbigenetic_mapregions_filesamples_filetargets_file

meta versions roh

roh:

A program for detecting runs of homo/autozygosity. Only bi-allelic sites are considered.

Sorts VCF files

metavcf

meta versions vcf

sort:

Sort VCF files by coordinates.

Split a vcf file into files per chromosome

metavcftbi

meta split_vcf versions

bcftools:

Sort VCF files by coordinates.

Generates stats from VCF files

metavcftbiregionstargetssamplesexonsfasta

meta stats versions

stats:

Parses VCF or BCF and produces text file stats which is suitable for machine processing and can be plotted using plot-vcfstats.

View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF

metavcfindexregionstargetssamples

meta vcf versions

view:

View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF

Demultiplex Illumina BCL files

metasamplesheetrun_dir

versions fastq fastq_idx undetermined undetermined_idx reports stats interop

Demultiplex Illumina BCL files

metasamplesheetrun_dir

versions fastq fastq_idx undetermined undetermined_idx reports logs interop

Beagle v5.2 is a software package for phasing genotypes and for imputing ungenotyped markers.

metavcfrefgenmapexclsamplesexclmarkers

meta versions vcf log

beagle5:

Beagle is a software package for phasing genotypes and for imputing ungenotyped markers.

Convert a BED file to a VCF file according to a YAML config

metabedconfigmeta2fai

meta versions vcf

Converts a bam file to a bed12 file.

metabam

meta bed versions

bedtools:

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

For each feature in A, finds the closest feature (upstream or downstream) in B.

metainput_1input_2fasta_fai

meta versions output

bedtools:

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

Returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file.

metabedsizes

meta bed versions

bedtools:

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

computes both the depth and breadth of coverage of features in file B on the features in file A

metainput_Ainput_Bgenome_file

meta bed versions

bedtools:

A powerful toolset for genome arithmetic

Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences) for a given genome.

metaintervalsscalesizesextension

meta genomecov versions

bedtools:

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

extract sequences in a FASTA file based on intervals defined in a feature file.

bedfasta

fasta versions

bedtools:

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

Groups features in a BED file by given column(s) and computes summary statistics for each group to another column.

metabedsummary_column

meta bed versions

bedtools:

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

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

metaintervals1intervals2meta2chrom_sizes

meta intersect versions

bedtools:

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

Calculate Jaccard statistic b/w two feature files.

metainput_ainput_bmeta2genome_file

meta versions tsv

bedtools:

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

Makes adjacent or sliding windows across a genome or BED file.

metaregions

meta versions bed

bedtools:

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

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

metaintervals1intervals2meta2chrom_sizes

meta mapped versions

bedtools:

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

masks sequences in a FASTA file based on intervals defined in a feature file.

metabedfasta

meta fasta versions

bedtools:

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

combines overlapping or “book-ended” features in an interval file into a single feature which spans all of the combined features.

metabed

meta bed versions

bedtools:

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

Identifies common intervals among multiple (and subsets thereof) sorted BED/GFF/VCF files.

metabedschrom_sizes

meta versions bed

bedtools:

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

Shifts each feature by specific number of bases

metabedchrom_sizes

meta bed versions

bedtools:

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

Adds a specified number of bases in each direction (unique values may be specified for either -l or -r)

metabed

meta bed versions

bedtools:

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

Sorts a feature file by chromosome and other criteria.

metaintervalsgenome_file

meta sorted versions

bedtools:

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

Split BED files into several smaller BED files

metabed

meta versions beds

bedtools:

A powerful toolset for genome arithmetic

Finds overlaps between two sets of regions (A and B), removes the overlaps from A and reports the remaining portion of A.

metaintervals1intervals2

meta 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

metabedgraphmeta2chrom_sizes

meta bed versions

bedtools:

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

Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats.

metainput

meta versions output

Locate and tag duplicate reads in a BAM file

metabam

meta bam metrics versions

biobambam:

biobambam is a set of tools for early stage alignment file processing.

Merge a list of sorted bam files

metabam

meta bam bam_index checksum versions

biobambam:

biobambam is a set of tools for early stage alignment file processing.

Parallel sorting and duplicate marking

metabamsmeta2fasta

meta bam bam_index cram metrics versions

biobambam:

biobambam is a set of tools for early stage alignment file processing.

Use k-mers to rapidly subtype S. enterica genomes

metaseqsscheme_metadata

meta versions summary kmer_results simple_summary

Aligns single- or paired-end reads from bisulfite-converted libraries to a reference genome using Biscuit.

metareadsindex

meta bam bai versions

biscuit:

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

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

metareadsindex

meta 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.

Summarize and/or filter reads based on bisulfite conversion rate

metabambaiindex

meta bsconv_bam versions

biscuit:

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

Summarizes read-level methylation (and optionally SNV) information from a Biscuit BAM file in a standard-compliant BED format.

metabambaisnp_bedindex

meta epiread_bed versions

biscuit:

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

Indexes a reference genome for use with Biscuit

fasta

index versions

biscuit:

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

Merges methylation information for opposite-strand C's in a CpG context

metabedindex

meta mergecg_bed versions

biscuit:

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

Computes cytosine methylation and callable SNV mutations, optionally in reference to a germline BAM to call somatic variants

metanormal_bamsnormal_baistumor_bamtumor_baiindex

meta versions vcf

biscuit:

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

Perform basic quality control on a BAM file generated with Biscuit

metabam

biscuit_qc_reports versions

biscuit:

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

Summarizes methylation or SNV information from a Biscuit VCF in a standard-compliant BED file.

metavcf

meta bed versions

biscuit:

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

Performs alignment of BS-Seq reads using bismark

metareadsindex

meta bam unmapped 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.

Relates methylation calls back to genomic cytosine contexts.

metacoverage_fileindex

meta 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.

metabam

meta 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.

fasta

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.

metabamindex

meta 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

metaalign_reportsplitting_reportdedup_reportmbiasfasta

meta 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.

bamalign_reportdedup_reportsplitting_reportmbias

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.

Queries a BLAST DNA database

metafastameta2db

meta txt versions

blast:

BLAST finds regions of similarity between biological sequences.

BLASTP (Basic Local Alignment Search Tool- Protein) compares an amino acid (protein) query sequence against a protein database

metafastameta2dbout_ext

meta xml tsv csv versions

blast:

BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit.

Builds a BLAST database

metafasta

meta db versions

blast:

BLAST finds regions of similarity between biological sequences.

Queries a BLAST DNA database

metafastameta2db

meta txt versions

blast:

Protein to Translated Nucleotide BLAST.

Queries a sequence subject

metaquerymeta2subject

meta versions psl

Align reads to a reference genome using bowtie

metareadsindex

bam versions fastq

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

fasta

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

metareadsmeta2indexsave_unalignedsort_bam

aligned versions fastq log

bowtie2:

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

Builds bowtie index for reference genome

metafasta

meta index versions

bowtie2:

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

Re-estimate taxonomic abundance of metagenomic samples analyzed by kraken.

metakraken_reportdatabase

meta versions reports txt

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.

Combine output of metagenomic samples analyzed by bracken.

metainput

meta versions txt

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.

Benchmarking Universal Single Copy Orthologs

metafastamodelineagebusco_lineages_pathconfig_file

meta batch_summary short_summaries_txt short_summaries_json busco_dir full_table missing_busco_list single_copy_proteins seq_dir translated_proteins versions

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

metareadsmeta2index

meta versions sai

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

metafasta

meta 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

metareadsmeta2indexsort_bam

bam 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

metareadssaimeta2index

meta versions bam

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

metareadssaimeta2index

meta versions bam

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

metafasta

meta 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

metareadsmeta2indexsort_bam

meta bam versions

bwa:

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

Performs alignment of BS-Seq reads using bwameth

metareadsindex

meta bam versions

bwameth:

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