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.

  • alignment 3
  • peak-calling 3
  • atac-seq 3
  • chip-seq 3
  • ATAC-seq 2
  • ChIP-seq 2
  • bam 1
  • fastq 1
  • sam 1
  • map 1
  • convert 1
  • trimming 1
  • QC 1
  • peaks 1
  • tabular 1
  • gsea 1
  • hi-c 1
  • chip 1
  • duplicate removal 1
  • chromap 1
  • IDR 1
  • ChIP-Seq 1
  • phantom peaks 1
  • fasta 0
  • vcf 0
  • genomics 0
  • metagenomics 0
  • genome 0
  • index 0
  • reference 0
  • bed 0
  • gatk4 0
  • assembly 0
  • cram 0
  • sort 0
  • structural variants 0
  • variant calling 0
  • database 0
  • annotation 0
  • align 0
  • merge 0
  • filter 0
  • gff 0
  • bacteria 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
  • imputation 0
  • bedtools 0
  • phylogeny 0
  • graph 0
  • isoseq 0
  • gvcf 0
  • build 0
  • reporting 0
  • bcftools 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
  • compression 0
  • indexing 0
  • kmer 0
  • 5mC 0
  • antimicrobial resistance 0
  • phage 0
  • mapping 0
  • long-read 0
  • imaging 0
  • metrics 0
  • stats 0
  • serotype 0
  • tsv 0
  • visualisation 0
  • demultiplex 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
  • genotype 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
  • 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
  • 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
  • circrna 0
  • haplotypecaller 0
  • bedgraph 0
  • genmod 0
  • SV 0
  • ranking 0
  • compress 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
  • 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
  • bgzip 0
  • ccs 0
  • hmmcopy 0
  • DNA sequence 0
  • reference-free 0
  • microsatellite 0
  • reads 0
  • quantification 0
  • ngscheckmate 0
  • containment 0
  • matching 0
  • HiFi 0
  • preprocessing 0
  • happy 0
  • reports 0
  • notebook 0
  • bedpe 0
  • gatk4spark 0
  • mzml 0
  • somatic variants 0
  • ligate 0
  • amplicon sequences 0
  • mtDNA 0
  • windowmasker 0
  • pseudoalignment 0
  • krona chart 0
  • 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
  • tabix 0
  • spaceranger 0
  • subsample 0
  • UMI 0
  • informative sites 0
  • kinship 0
  • identity 0
  • relatedness 0
  • lossless 0
  • small indels 0
  • observations 0
  • shapeit 0
  • scores 0
  • zip 0
  • 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
  • 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
  • image_analysis 0
  • cellranger 0
  • bakta 0
  • genomes 0
  • deeparg 0
  • C to T 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
  • tbi 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
  • gem 0
  • allele 0
  • sage 0
  • vcflib/vcffixup 0
  • umicollapse 0
  • trimfq 0
  • nanopore sequencing 0
  • scRNA-Seq 0
  • morphology 0
  • resegment 0
  • AC/NS/AF 0
  • files 0
  • relabel 0
  • hostile 0
  • Pacbio 0
  • adapterremoval 0
  • cell segmentation 0
  • upd 0
  • uniparental 0
  • disomy 0
  • snv 0
  • downsample 0
  • downsample bam 0
  • antimicrobial reistance 0
  • mkarv 0
  • decontamination 0
  • atlas 0
  • contiguate 0
  • scanpy 0
  • Mycobacterium tuberculosis 0
  • chromosomal rearrangements 0
  • eucaryotes 0
  • extension 0
  • coding 0
  • cds 0
  • transcroder 0
  • sequencing adapters 0
  • bedgraphtobigwig 0
  • rna velocity 0
  • bigbed 0
  • bedtobigbed 0
  • genepred 0
  • refflat 0
  • gtftogenepred 0
  • ucsc/liftover 0
  • cobra 0
  • metagenome assembler 0
  • vcf2db 0
  • human removal 0
  • subsample bam 0
  • lua 0
  • gemini 0
  • logFC 0
  • pangenome-scale 0
  • all versus all 0
  • mashmap 0
  • wavefront 0
  • whamg 0
  • wham 0
  • bwameme 0
  • HLA 0
  • copy-number 0
  • grabix 0
  • bwamem2 0
  • copy number analysis 0
  • subsetting 0
  • pile up 0
  • barcodes 0
  • doublet_detection 0
  • gender determination 0
  • ribosomal 0
  • copy number alterations 0
  • 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
  • dbnsfp 0
  • predictions 0
  • updatedata 0
  • run 0
  • pdb 0
  • SNPs 0
  • CRAM 0
  • gnu 0
  • busco 0
  • sha256 0
  • relative coverage 0
  • lifestyle 0
  • MMseqs2 0
  • catpack 0
  • rare variants 0
  • error 0
  • transposable element 0
  • de-novo 0
  • Computational Immunology 0
  • longread 0
  • generic 0
  • sliding window 0
  • 256 bit 0
  • Bioinformatics Tools 0
  • Immune Deconvolution 0
  • shinyngs 0
  • doublet 0
  • exploratory 0
  • boxplot 0
  • density 0
  • features 0
  • coreutils 0
  • hamming-distance 0
  • invariant 0
  • fast5 0
  • recovery 0
  • ATLAS 0
  • detecting svs 0
  • short-read sequencing 0
  • lexogen 0
  • sylph 0
  • mgi 0
  • sequencing_bias 0
  • svtk/baftest 0
  • baftest 0
  • countsvtypes 0
  • genotype-based demultiplexing 0
  • variantcalling 0
  • donor deconvolution 0
  • rdtest2vcf 0
  • rdtest 0
  • split_kmers 0
  • vcf2bed 0
  • leafcutter 0
  • decompress 0
  • post mortem damage 0
  • polya tail 0
  • mapad 0
  • bias 0
  • sccmec 0
  • constant 0
  • overlap-based merging 0
  • cycif 0
  • background 0
  • single-stranded 0
  • ancientDNA 0
  • rRNA 0
  • ribosomal RNA 0
  • check 0
  • authentict 0
  • block substitutions 0
  • decomposeblocksub 0
  • signatures 0
  • streptococcus 0
  • hash sketch 0
  • identity-by-descent 0
  • fracminhash sketch 0
  • read group 0
  • paired reads merging 0
  • translation 0
  • spatype 0
  • functional enrichment 0
  • spa 0
  • droplet based single cells 0
  • geo 0
  • c to t 0
  • adna 0
  • script 0
  • standard 0
  • clahe 0
  • install 0
  • joint-genotyping 0
  • genotypegvcf 0
  • realign 0
  • model 0
  • svg 0
  • xml 0
  • circular 0
  • spot 0
  • introns 0
  • java 0
  • rank 0
  • AMPs 0
  • parallel 0
  • hashing-based deconvolution 0
  • Staphylococcus aureus 0
  • plastid 0
  • tag2tag 0
  • resfinder 0
  • resistance genes 0
  • haplotag 0
  • quality check 0
  • raw 0
  • association 0
  • bam2fastx 0
  • bam2fastq 0
  • immcantation 0
  • airrseq 0
  • immunoinformatics 0
  • co-orthology 0
  • homology 0
  • sequence similarity 0
  • spectral clustering 0
  • comparative genomics 0
  • microRNA 0
  • size 0
  • deep variant 0
  • mutect 0
  • idx 0
  • affy 0
  • refresh 0
  • cram-size 0
  • Staging 0
  • staging 0
  • transform 0
  • gaps 0
  • tags 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
  • impute-info 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
  • setgt 0
  • tnseq 0
  • shift 0
  • scimap 0
  • spatial_neighborhoods 0
  • decoy 0
  • associations 0
  • htseq 0
  • rrna 0
  • installation 0
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  • amino acid 0
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  • genomes on a tree 0
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  • low coverage 0
  • antibody capture 0
  • antigen capture 0
  • Sample 0
  • Haplotypes 0
  • Imputation 0
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  • GNU 0
  • merge compare 0
  • multiomics 0
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  • tama_collapse.py 0
  • mkvdjref 0
  • gene model 0
  • TAMA 0
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  • 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
  • genome profile 0
  • compound 0
  • models 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
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  • 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
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  • annotations 0
  • pos 0
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  • igv 0
  • igv.js 0
  • js 0
  • genome browser 0
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  • spliced 0
  • SRA 0
  • TMA dearray 0
  • UNet 0
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  • str 0
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  • antibiotic resistance genes 0
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  • ANI 0
  • enzyme 0
  • digest 0
  • cload 0
  • ENA 0
  • Cores 0
  • public 0
  • cooler/balance 0
  • consensus sequence 0
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  • single molecule 0
  • generate 0
  • random 0
  • Segmentation 0
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  • 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
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  • snvs 0
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  • 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
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  • 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
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  • 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
  • csi 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
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  • interleave 0
  • temperate 0
  • header 0
  • seq 0
  • selection 0
  • random draw 0
  • pseudohaploid 0
  • pseudodiploid 0
  • freqsum 0
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  • gc_wiggle 0
  • readgroup 0
  • paired 0
  • rhocall 0
  • pedfilter 0
  • R 0
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  • bamtools/convert 0
  • strandedness 0
  • experiment 0
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  • inner_distance 0
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  • integrity 0
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  • rocplot 0
  • repair 0
  • rtg-tools 0
  • salsa 0
  • salsa2 0
  • LCA 0
  • Ancestor 0
  • multimapper 0
  • flagstat 0
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  • duplicate marking 0
  • amplicon 0
  • ampliconclip 0
  • calmd 0
  • faidx 0
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  • 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
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  • 3D heat map 0
  • Merqury 0
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  • overlap 0
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  • HLA-I 0
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  • update header 0
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  • ligation junctions 0
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  • gender 0
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Performs preprocessing and alignment of chromatin fastq files to fasta reference files using chromap.

0101010000

bed bam tagAlign pairs versions

chromap:

Fast alignment and preprocessing of chromatin profiles

Make a GSEA class file (.chip) from tabular inputs

0101

chip versions

custom:

Make a GSEA annotation file (.chip) from tabular inputs

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

0120

peak versions bedgraph_pvalues bedgraph_pileup bed_intervals duplicates

Measures reproducibility of ChIP-seq, ATAC-seq peaks using IDR (Irreproducible Discovery Rate)

000

idr log png versions

Peak calling of enriched genomic regions of ChIP-seq and ATAC-seq experiments

0120

peak xls versions gapped bed bdg

macs2:

Model Based Analysis for ChIP-Seq data

Peak calling of enriched genomic regions of ChIP-seq and ATAC-seq experiments

0120

peak xls versions gapped bed bdg

macs3:

Model Based Analysis for ChIP-Seq data

"This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays."

01

spp pdf rdata versions

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