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.

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

Converts certain output formats to VCF

012010

vcf_gz vcf bcf_gz bcf hap legend samples tbi csi versions

bcftools:

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.

Index VCF tools

01

csi tbi versions

bcftools:

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.

Adds imputation information metrics to the INFO field based on selected FORMAT tags. Only the IMPUTE2 INFO metric from FORMAT/GP tags is currently available.

01200

vcf tbi csi versions

bcftools:

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.

bcftools plugin impute-info:

Bcftools plugins are tools that can be used with bcftools to manipulate variant calls in Variant Call Format (VCF) and BCF. The impute-info plugin adds imputation information metrics to the INFO field based on selected FORMAT tags. Only the IMPUTE2 INFO metric from FORMAT/GP tags is currently available

Sets genotypes according to the specified criteria and filtering expressions. For example, missing genotypes can be set to ref, but much more than that.

0120000

vcf tbi csi versions

bcftools:

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.

bcftools plugin setGT:

Bcftools plugins are tools that can be used with bcftools to manipulate variant calls in Variant Call Format (VCF) and BCF. The setGT plugin sets genotypes according to the specified criteria and filtering expressions. For example, missing genotypes can be set to ref, but much more than that.

Checks if the input file is bgzip compressed or not

01

compress_bgzip versions

grabix:

a wee tool for random access into BGZF files.

Demultiplex bgzip'd fastq files

012

sample_fastq metrics most_frequent_unmatched per_project_metrics per_sample_metrics sample_barcode_hop_metrics versions

Compresses/decompresses files

01

output gzi versions

bgzip:

Bgzip compresses or decompresses files in a similar manner to, and compatible with, gzip.

bgzip a sorted tab-delimited genome file and then create tabix index

01

gz_tbi gz_csi versions

tabix:

Generic indexer for TAB-delimited genome position files.

create tabix index from a sorted bgzip tab-delimited genome file

01

tbi csi versions

tabix:

Generic indexer for TAB-delimited genome position files.

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