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.

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

Demultiplex Illumina BCL files

012

fastq fastq_idx undetermined undetermined_idx reports stats interop versions

Demultiplex Illumina BCL files

012

fastq fastq_idx undetermined undetermined_idx reports logs interop versions

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.

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

012

bed versions

bedtools:

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

Perform basic quality control on a BAM file generated with Biscuit

010101

reports versions

biscuit:

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

Collects bismark alignment reports

01234

report versions

bismark:

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

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

010

reports txt versions

bracken:

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

Module to create FASTQs needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkfastq command.

012

fastq undetermined_fastq reports stats interop versions

cellranger:

Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.

Creates Kraken-style reports from centrifuge out files

010

kreport versions

centrifuge:

Centrifuge is a classifier for metagenomic sequences.

Datavzrd is a tool to create visual HTML reports from collections of CSV/TSV tables.

0

report versions

DeepSomatic is an extension of deep learning-based variant caller DeepVariant that takes aligned reads (in BAM or CRAM format) from tumor and normal data, produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports somatic variants in a standard VCF or gVCF file.

0123401010101

vcf vcf_tbi gvcf gvcf_tbi versions

Gathers scattered BQSR recalibration reports into a single file

01

table versions

gatk4:

Genome Analysis Toolkit (GATK4)

Tool to summarize and combine all hAMRonization reports into a single file

00

json tsv html versions

hamronization:

Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification

A Python application to generate self-contained HTML reports for variant review and other genomic applications

0123012

report versions

Render jupyter (or jupytext) notebooks to HTML reports. Supports parametrization through papermill.

0100

report artifacts versions

jupytext:

Jupyter notebooks as plain text scripts or markdown documents

papermill:

Parameterize, execute, and analyze notebooks

nbconvert:

Parameterize, execute, and analyze notebooks

Takes multiple kraken-style reports and combines them into a single report file

01

txt versions

krakentools:

KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs.

Demultiplex MGI fastq files

012

fastq undetermined ambiguous undetermined_reports ambiguous_reports general_info_reports index_reports sample_stat_reports qc_reports versions

mgikit demultiplex:

Demultiplex MGI fastq files

Computes tier-based cutoffs from a sample-specific error model which is generated by muse/call and reports the finalized variants

01012

vcf versions

MuSE:

Somatic point mutation caller based on Markov substitution model for molecular evolution

NACHO (NAnostring quality Control dasHbOard) is developed for NanoString nCounter data. NanoString nCounter data is a messenger-RNA/micro-RNA (mRNA/miRNA) expression assay and works with fluorescent barcodes. Each barcode is assigned a mRNA/miRNA, which can be counted after bonding with its target. As a result each count of a specific barcode represents the presence of its target mRNA/miRNA.

0101

nacho_qc_reports nacho_qc_png nacho_qc_txt versions

NACHO:

R package that uses two main functions to summarize and visualize NanoString RCC files, namely: load_rcc() and visualise(). It also includes a function normalise(), which (re)calculates sample specific size factors and normalises the data. For more information vignette("NACHO") and vignette("NACHO-analysis")

Nanoq implements ultra-fast read filters and summary reports for high-throughput nanopore reads.

010

stats reads versions

Generate summary reports with raw data for Nonpareil NPO curves, including MultiQC compatible JSON/TSV files

01

json tsv csv pdf versions

nonpareil:

Estimate average coverage and create curves for metagenomic datasets

Render a Quarto notebook, including parametrization.

01000

html notebook artifacts params_yaml extensions versions

papermill:

Parameterize, execute, and analyze notebooks

Render an rmarkdown notebook. Supports parametrization.

0100

report parameterised_notebook artifacts session_info versions

rmarkdown:

Dynamic Documents for R

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

012

idxstats versions

samtools:

SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.

A tool of the wipertools suite that merges wiping reports generated by wipertools_fastqwiper

01

gathered_report versions

reportgather:

A tool of the wipertools suite that merges wiping reports generated by wipertools_fastqwiper.

Click here to trigger an update.