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.

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

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

012000

genomecov versions

bedtools:

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

Combines multiple BedGraph files into a single file

0101

bed versions

bedtools:

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

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.

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.

Copy number and genotype annotation from whole genome and whole exome sequencing data

0123456000000000

bedgraph control_cpn sample_cpn gcprofile_cpn BAF CNV info ratio config versions

controlfreec/freec:

Copy number and genotype annotation from whole genome and whole exome sequencing data.

This tool takes an alignment of reads or fragments as input (BAM file) and generates a coverage track (bigWig or bedGraph) as output.

01200

bigwig bedgraph versions

deeptools:

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

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 mappability files for a genome

0101

wig bedgraph txt csv versions

genmap:

Ultra-fast computation of genome mappability.

Peak-calling for ChIP-seq and ATAC-seq enrichment experiments

0120

peak versions bedgraph_pvalues bedgraph_pileup bed_intervals duplicates

Create a UCSC bed graph with the HOMER suite

01

bedGraph versions

homer:

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

Extracts per-base methylation metrics from alignments

01200

bedgraph methylkit versions

methyldackel:

Methylation caller from MethylDackel, a (mostly) universal methylation extractor for methyl-seq experiments.

A bioinformatics tool for working with modified bases

0120101

bed bedgraph log versions

modkit:

A bioinformatics tool for working with modified bases in Oxford Nanopore sequencing data

Call peaks using SEACR on sequenced reads in bedgraph format

0120

bed versions

seacr:

SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by "zeroes" (i.e. regions with no read coverage).

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.

Searches a genome for a telomere string such as TTAGGG

010

tsv bedgraph versions

tidk:

tidk is a toolkit to identify and visualise telomeric repeats in genomes

Remove lines from bed file that refer to off-chromosome locations.

010

bedgraph versions

ucsc:

Remove lines from bed file that refer to off-chromosome locations.

Convert a bedGraph file to bigWig format.

010

bigwig versions

ucsc:

Convert a bedGraph file to bigWig format.

compute average score of bigwig over bed file

010

tab versions

ucsc:

Compute average score of big wig over each bed, which may have introns.

Convert ascii format wig file to binary big wig format

010

bw versions

ucsc:

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

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