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.

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

010

singles_truncated discarded paired_truncated collapsed collapsed_truncated paired_interleaved settings versions

Merging overlapping paired reads into a single read.

010

merged unmerged ihist versions log

bbmap:

BBMap is a short read aligner, as well as various other bioinformatic tools.

Allows one to screen for overlaps between two sets of genomic features.

01201

intersect versions

bedtools:

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

Allows one to screen for overlaps between two sets of genomic features.

01201

mapped versions

bedtools:

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

combines overlapping or โ€œbook-endedโ€ features in an interval file into a single feature which spans all of the combined features.

01

bed 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.

Cut up fasta file in non-overlapping or overlapping parts of equal length.

010

fasta bed versions

concoct:

Clustering cONtigs with COverage and ComposiTion

Adds predicted functional consequence, gene overlap, and noncoding element overlap annotations to SV VCF from GATK-SV pipeline. Input files are an SV VCF, a GTF file containing primary or canonical transcripts, and a BED file containing noncoding elements. Output file is an annotated SV VCF.

0123000

annotated_vcf index versions

gatk4:

Genome Analysis Toolkit (GATK4)

Whole-genome assembly using PacBio HiFi reads

012012012

raw_unitigs corrected_reads source_overlaps reverse_overlaps processed_contigs processed_unitigs primary_contigs alternate_contigs paternal_contigs maternal_contigs log versions

gcCounter function from HMMcopy utilities, used to generate GC content in non-overlapping windows from a fasta reference

01

wig versions

hmmcopy:

C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy

mapCounter function from HMMcopy utilities, used to generate mappability in non-overlapping windows from a bigwig file

01

wig versions

hmmcopy:

C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy

Software to pileup reads and corresponding base quality for each overlapping SNPs and each barcode.

012

cel plp var umi versions

popscle:

A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxiliary tools

Calculate coverage cutoffs to determine when to purge duplicated sequence.

01

cutoff log versions

purgedups:

Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth

Separates out sequences purged of falsely duplicated sequences.

012

haplotigs purged versions

purgedups:

Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth

Plots the read coverage from a purge dups statistics file and cutoffs.

012

png versions

purgedups:

Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth

Create read depth histogram and base-level read depth for an assembly based on pacbio data

01

stat basecov versions

purgedups:

Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth

Purge haplotigs and overlaps for an assembly

0123

bed log versions

purgedups:

Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth

Split fasta file by 'N's to aid in self alignment for duplicate purging

01

split_fasta versions

purgedups:

Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth

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