Available Modules

Modules are the building stones of all DSL2 nf-core blocks. You can find more info from nf-core website, if you would like to write your own module.

  • vcf 11
  • structural variants 8
  • benchmark 5
  • sv 4
  • happy 4
  • binning 3
  • haplotype 3
  • validation 3
  • bin 3
  • vrhyme 3
  • survivor 3
  • comparisons 3
  • protein 2
  • structure 2
  • comparison 2
  • instrain 2
  • rtgtools 2
  • bam 1
  • fasta 1
  • fastq 1
  • metagenomics 1
  • bed 1
  • sam 1
  • align 1
  • merge 1
  • filter 1
  • statistics 1
  • coverage 1
  • somatic 1
  • conversion 1
  • phage 1
  • virus 1
  • bedGraph 1
  • diversity 1
  • compare 1
  • profile 1
  • normalization 1
  • bedpe 1
  • somatic variants 1
  • benchmarking 1
  • combine 1
  • ped 1
  • intersection 1
  • extractunbinned 1
  • linkbins 1
  • simulation 1
  • featuretable 1
  • extraction 1
  • sompy 1
  • population genomics 1
  • unionBedGraphs 1
  • rtg-tools 1
  • rtg 1
  • pedfilter 1
  • rocplot 1
  • genomics 0
  • genome 0
  • index 0
  • reference 0
  • alignment 0
  • assembly 0
  • gatk4 0
  • cram 0
  • sort 0
  • variant calling 0
  • annotation 0
  • database 0
  • gff 0
  • bacteria 0
  • map 0
  • qc 0
  • variants 0
  • quality control 0
  • classification 0
  • download 0
  • classify 0
  • gtf 0
  • nanopore 0
  • cnv 0
  • split 0
  • gfa 0
  • taxonomic profiling 0
  • k-mer 0
  • variant 0
  • MSA 0
  • contamination 0
  • pacbio 0
  • taxonomy 0
  • sentieon 0
  • convert 0
  • count 0
  • proteomics 0
  • quality 0
  • single-cell 0
  • VCF 0
  • copy number 0
  • clustering 0
  • ancient DNA 0
  • bedtools 0
  • imputation 0
  • phylogeny 0
  • contigs 0
  • bisulfite 0
  • mags 0
  • reporting 0
  • graph 0
  • variation graph 0
  • isoseq 0
  • build 0
  • bcftools 0
  • trimming 0
  • long reads 0
  • gvcf 0
  • kmer 0
  • cna 0
  • rnaseq 0
  • wgs 0
  • illumina 0
  • bqsr 0
  • databases 0
  • QC 0
  • compression 0
  • indexing 0
  • bisulphite 0
  • methylseq 0
  • picard 0
  • consensus 0
  • methylation 0
  • table 0
  • metrics 0
  • imaging 0
  • antimicrobial resistance 0
  • taxonomic classification 0
  • long-read 0
  • 5mC 0
  • mapping 0
  • visualisation 0
  • stats 0
  • demultiplex 0
  • openms 0
  • tsv 0
  • sequences 0
  • serotype 0
  • protein sequence 0
  • amr 0
  • base quality score recalibration 0
  • histogram 0
  • scWGBS 0
  • WGBS 0
  • pairs 0
  • DNA methylation 0
  • pangenome graph 0
  • markduplicates 0
  • bins 0
  • searching 0
  • depth 0
  • cluster 0
  • aDNA 0
  • plot 0
  • neural network 0
  • matrix 0
  • expression 0
  • checkm 0
  • LAST 0
  • metagenome 0
  • genotype 0
  • completeness 0
  • archaeogenomics 0
  • repeat 0
  • biscuit 0
  • mmseqs2 0
  • palaeogenomics 0
  • damage 0
  • bcf 0
  • mappability 0
  • filtering 0
  • annotate 0
  • db 0
  • bisulfite sequencing 0
  • cooler 0
  • bwa 0
  • aligner 0
  • low-coverage 0
  • samtools 0
  • iCLIP 0
  • machine learning 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
  • kraken2 0
  • glimpse 0
  • bismark 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
  • complexity 0
  • feature 0
  • json 0
  • demultiplexing 0
  • prediction 0
  • mirna 0
  • antimicrobial resistance genes 0
  • report 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
  • merging 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
  • counts 0
  • tabular 0
  • microbiome 0
  • extract 0
  • csv 0
  • sourmash 0
  • deamination 0
  • riboseq 0
  • MAF 0
  • isolates 0
  • de novo assembly 0
  • text 0
  • wxs 0
  • clipping 0
  • cut 0
  • genome assembler 0
  • CLIP 0
  • bedgraph 0
  • bcl2fastq 0
  • archaeogenetics 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
  • peak-calling 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
  • redundancy 0
  • union 0
  • ATAC-seq 0
  • family 0
  • bgzip 0
  • add 0
  • sketch 0
  • retrotransposon 0
  • BGC 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
  • ont 0
  • umitools 0
  • HiFi 0
  • hmmcopy 0
  • xeniumranger 0
  • ancestry 0
  • ccs 0
  • abundance 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
  • entrez 0
  • fastk 0
  • zip 0
  • npz 0
  • guide tree 0
  • RNA 0
  • repeat expansion 0
  • fcs-gx 0
  • fingerprint 0
  • PCA 0
  • miRNA 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
  • 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
  • reports 0
  • ligate 0
  • notebook 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
  • UMI 0
  • spaceranger 0
  • informative sites 0
  • kinship 0
  • identity 0
  • relatedness 0
  • lossless 0
  • observations 0
  • shapeit 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
  • kraken 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
  • mkfastq 0
  • bamtools 0
  • nucleotide 0
  • chromosome 0
  • prokaryotes 0
  • DRAMP 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
  • bracken 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
  • 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
  • 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
  • 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
  • trim 0
  • khmer 0
  • bustools 0
  • awk 0
  • salmon 0
  • BAM 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
  • krakentools 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
  • corrupted 0
  • emboss 0
  • nacho 0
  • interval list 0
  • nanostring 0
  • mRNA 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
  • fracminhash sketch 0
  • ribosomal RNA 0
  • hash sketch 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
  • 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
  • multiqc 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
  • cgMLST 0
  • WGS 0
  • redundant 0
  • nanoq 0
  • Read filters 0
  • Read trimming 0
  • Read report 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
  • mgi 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
  • quarto 0
  • python 0
  • r 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
  • 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
  • interproscan 0
  • genomic islands 0
  • insertion 0
  • postprocessing 0
  • jasminesv 0
  • jasmine 0
  • Python 0
  • Jupyter 0
  • jupytext 0
  • papermill 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
  • combining 0
  • bioawk 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
  • gatherbqsrreports 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
  • subtract 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
  • R 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
  • 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
  • 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
  • genomecov 0
  • illumina datasets 0
  • select 0
  • tumor/normal 0
  • hla-typing 0
  • ILP 0
  • HLA-I 0
  • block-compressed 0
  • update header 0
  • PCR/optical duplicates 0
  • flip 0
  • upper-triangular matrix 0
  • ligation junctions 0
  • pairtools 0
  • pairstools 0
  • restriction fragments 0
  • BCF 0
  • graph formats 0
  • paragraph 0
  • graphs 0
  • pbbam 0
  • pbmerge 0
  • subreads 0
  • pbp 0
  • pair-end 0
  • read 0
  • pedigrees 0
  • motif 0
  • ChIP-Seq 0
  • phantom peaks 0
  • prophage 0
  • identification 0
  • graph viz 0
  • graph unchopping 0
  • closest 0
  • contaminant 0
  • bamtobed 0
  • mosdepth 0
  • otu table 0
  • sorting 0
  • microsatellite instability 0
  • scan 0
  • mtnucratio 0
  • ratio 0
  • autozygosity 0
  • mitochondrial to nuclear ratio 0
  • bioinformatics tools 0
  • Beautiful stand-alone HTML report 0
  • GATK UnifiedGenotyper 0
  • SNP table 0
  • cancer genome 0
  • graph stats 0
  • somatic structural variations 0
  • mobile element insertions 0
  • sequencing summary 0
  • NextGenMap 0
  • ngm 0
  • Neisseria gonorrhoeae 0
  • gender 0
  • homozygosity 0
  • biallelic 0
  • graph construction 0
  • graph drawing 0
  • squeeze 0
  • odgi 0
  • combine graphs 0
  • taxonomic composition 0

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.

Create a database from protein structures

01

db versions

foldseek:

Foldseek: fast and accurate protein structure search

Search for protein structural hits against a foldseek database of protein structures

0101

aln versions

foldseek:

Foldseek: fast and accurate protein structure search

Somatic VCF Feature Extraction tool from hap.y.

012340101

features versions

happy:

Haplotype VCF comparison tools

Hap.py is a tool to compare diploid genotypes at haplotype level. Rather than comparing VCF records row by row, hap.py will generate and match alternate sequences in a superlocus. A superlocus is a small region of the genome (sized between 1 and around 1000 bp) that contains one or more variants.

012340101010101

summary_csv roc_all_csv roc_indel_locations_csv roc_indel_locations_pass_csv roc_snp_locations_csv roc_snp_locations_pass_csv extended_csv runinfo metrics_json vcf tbi versions

happy:

Haplotype VCF comparison tools

Pre.py is a preprocessing tool made to preprocess VCF files for Hap.py

0120101

preprocessed_vcf versions

happy:

Haplotype VCF comparison tools

Hap.py is a tool to compare diploid genotypes at haplotype level. som.py is a part of hap.py compares somatic variations.

012340101010101

features metrics stats versions

sompy:

Haplotype VCF comparison tools somatic variant comparison

Strain-level comparisons across multiple inStrain profiles

0120

compare comparisons_table pooled_snv snv_keys snv_info versions

instrain:

Calculation of strain-level metrics

inStrain is python program for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification

01000

profile snvs gene_info genome_info linkage mapping_info scaffold_info versions

instrain:

Calculation of strain-level metrics

Converts the contents of sequence data files (FASTA/FASTQ/SAM/BAM) into the RTG Sequence Data File (SDF) format.

0123

sdf versions

rtgtools:

RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation

Converts a PED file to VCF headers

01

output versions

rtgtools:

RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation

Plot ROC curves from vcfeval ROC data files, either to an image, or an interactive GUI. The interactive GUI isn't possible for nextflow.

01

png svg versions

rtgtools:

RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation

The VCFeval tool of RTG tools. It is used to evaluate called variants for agreement with a baseline variant set

012345601

tp_vcf tp_tbi fn_vcf fn_tbi fp_vcf fp_tbi baseline_vcf baseline_tbi snp_roc non_snp_roc weighted_roc summary phasing versions

rtgtools:

RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation

Converts a bedpe file to a VCF file (beta version)

01

vcf versions

survivor:

Toolset for SV simulation, comparison and filtering

Filter a vcf file based on size and/or regions to ignore

0120000

vcf versions

survivor:

Toolset for SV simulation, comparison and filtering

Compare or merge VCF files to generate a consensus or multi sample VCF files.

01000000

vcf versions

survivor:

Toolset for SV simulation, comparison and filtering

Simulate an SV VCF file based on a reference genome

01010100

parameters vcf bed fasta insertions versions

survivor:

Toolset for SV simulation, comparison and filtering

Report multiple stats over a VCF file

01000

stats versions

survivor:

Toolset for SV simulation, comparison and filtering

Given baseline and comparison sets of variants, calculate the recall/precision/f-measure

0123450101

fn_vcf fn_tbi fp_vcf fp_tbi tp_base_vcf tp_base_tbi tp_comp_vcf tp_comp_tbi summary versions

truvari:

Structural variant comparison tool for VCFs

Over multiple vcfs, calculate their intersection/consistency.

01

consistency versions

truvari:

Structural variant comparison tool for VCFs

Normalization of SVs into disjointed genomic regions

01

vcf versions

truvari:

Structural variant comparison tool for VCFs

Extracting sequences that were unbinnned by vRhyme into a FASTA file

0101

unbinned_sequences versions

vrhyme:

vRhyme functions by utilizing coverage variance comparisons and supervised machine learning classification of sequence features to construct viral metagenome-assembled genomes (vMAGs).

Linking bins output by vRhyme to create one sequences per bin

01

linked_bins versions

vrhyme:

vRhyme functions by utilizing coverage variance comparisons and supervised machine learning classification of sequence features to construct viral metagenome-assembled genomes (vMAGs).

Binning virus genomes from metagenomes

0101

bins membership summary versions

vrhyme:

vRhyme functions by utilizing coverage variance comparisons and supervised machine learning classification of sequence features to construct viral metagenome-assembled genomes (vMAGs).

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