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.

  • reference 5
  • illumina 5
  • fastq 4
  • bcl2fastq 4
  • mkfastq 3
  • single-cell 2
  • cellranger 2
  • immunoprofiling 2
  • index 1
  • align 1
  • demultiplex 1
  • samplesheet 1
  • vdj 1
  • bclconvert 1
  • mkvdjref 1
  • bam 0
  • fasta 0
  • vcf 0
  • genomics 0
  • metagenomics 0
  • genome 0
  • alignment 0
  • assembly 0
  • bed 0
  • gatk4 0
  • cram 0
  • sam 0
  • sort 0
  • variant calling 0
  • structural variants 0
  • annotation 0
  • database 0
  • merge 0
  • filter 0
  • gff 0
  • map 0
  • bacteria 0
  • statistics 0
  • coverage 0
  • qc 0
  • variants 0
  • quality control 0
  • gtf 0
  • download 0
  • classification 0
  • classify 0
  • cnv 0
  • nanopore 0
  • split 0
  • contamination 0
  • MSA 0
  • gfa 0
  • taxonomic profiling 0
  • k-mer 0
  • variant 0
  • taxonomy 0
  • sentieon 0
  • somatic 0
  • pacbio 0
  • convert 0
  • binning 0
  • quality 0
  • proteomics 0
  • count 0
  • conversion 0
  • clustering 0
  • copy number 0
  • VCF 0
  • ancient DNA 0
  • bedtools 0
  • imputation 0
  • phylogeny 0
  • contigs 0
  • bisulfite 0
  • reporting 0
  • graph 0
  • trimming 0
  • bcftools 0
  • sv 0
  • variation graph 0
  • gvcf 0
  • isoseq 0
  • build 0
  • cna 0
  • long reads 0
  • rnaseq 0
  • wgs 0
  • bqsr 0
  • databases 0
  • mags 0
  • protein 0
  • QC 0
  • indexing 0
  • compression 0
  • bisulphite 0
  • methylseq 0
  • picard 0
  • methylation 0
  • consensus 0
  • kmer 0
  • table 0
  • imaging 0
  • metrics 0
  • antimicrobial resistance 0
  • long-read 0
  • phage 0
  • 5mC 0
  • mapping 0
  • visualisation 0
  • stats 0
  • openms 0
  • tsv 0
  • serotype 0
  • sequences 0
  • base quality score recalibration 0
  • amr 0
  • taxonomic classification 0
  • searching 0
  • protein sequence 0
  • scWGBS 0
  • WGBS 0
  • haplotype 0
  • pairs 0
  • DNA methylation 0
  • markduplicates 0
  • bins 0
  • depth 0
  • pangenome graph 0
  • histogram 0
  • cluster 0
  • aDNA 0
  • structure 0
  • neural network 0
  • plot 0
  • matrix 0
  • expression 0
  • db 0
  • LAST 0
  • checkm 0
  • metagenome 0
  • genotype 0
  • completeness 0
  • archaeogenomics 0
  • repeat 0
  • biscuit 0
  • mmseqs2 0
  • palaeogenomics 0
  • virus 0
  • damage 0
  • bcf 0
  • mappability 0
  • filtering 0
  • annotate 0
  • validation 0
  • machine learning 0
  • transcript 0
  • bwa 0
  • cooler 0
  • low-coverage 0
  • samtools 0
  • iCLIP 0
  • bisulfite sequencing 0
  • aligner 0
  • mag 0
  • hmmsearch 0
  • gff3 0
  • decompression 0
  • segmentation 0
  • mkref 0
  • dedup 0
  • peaks 0
  • population genetics 0
  • phasing 0
  • msa 0
  • transcriptome 0
  • kraken2 0
  • glimpse 0
  • blast 0
  • bismark 0
  • example 0
  • evaluation 0
  • genotyping 0
  • complexity 0
  • seqkit 0
  • ncbi 0
  • spatial 0
  • sequence 0
  • germline 0
  • newick 0
  • umi 0
  • ucsc 0
  • gene 0
  • mirna 0
  • demultiplexing 0
  • tumor-only 0
  • differential 0
  • antimicrobial resistance genes 0
  • report 0
  • bedGraph 0
  • deduplication 0
  • prediction 0
  • vsearch 0
  • json 0
  • antimicrobial peptides 0
  • cnvkit 0
  • low frequency variant calling 0
  • prokaryote 0
  • scRNA-seq 0
  • kmers 0
  • single 0
  • pangenome 0
  • hmmer 0
  • snp 0
  • mitochondria 0
  • duplicates 0
  • NCBI 0
  • short-read 0
  • splicing 0
  • multiple sequence alignment 0
  • feature 0
  • gzip 0
  • plasmid 0
  • summary 0
  • kallisto 0
  • fragment 0
  • merging 0
  • amps 0
  • adapters 0
  • visualization 0
  • benchmark 0
  • de novo 0
  • single cell 0
  • arg 0
  • call 0
  • mem 0
  • svtk 0
  • 3-letter genome 0
  • ptr 0
  • gridss 0
  • coptr 0
  • detection 0
  • query 0
  • deamination 0
  • de novo assembly 0
  • counts 0
  • mpileup 0
  • microbiome 0
  • extract 0
  • indels 0
  • interval 0
  • csv 0
  • sourmash 0
  • diversity 0
  • tabular 0
  • riboseq 0
  • isolates 0
  • clipping 0
  • profiling 0
  • view 0
  • MAF 0
  • text 0
  • idXML 0
  • wxs 0
  • antibiotic resistance 0
  • mutect2 0
  • SV 0
  • CLIP 0
  • interval_list 0
  • haplotypecaller 0
  • cut 0
  • bin 0
  • genome assembler 0
  • circrna 0
  • bedgraph 0
  • gsea 0
  • fgbio 0
  • compare 0
  • read depth 0
  • miscoding lesions 0
  • ganon 0
  • archaeogenetics 0
  • hic 0
  • palaeogenetics 0
  • STR 0
  • phylogenetic placement 0
  • structural 0
  • profile 0
  • genmod 0
  • diamond 0
  • public datasets 0
  • bigwig 0
  • compress 0
  • peak-calling 0
  • snps 0
  • enrichment 0
  • ranking 0
  • deep learning 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
  • hmmcopy 0
  • DNA sequence 0
  • reference-free 0
  • microsatellite 0
  • reads 0
  • quantification 0
  • ngscheckmate 0
  • containment 0
  • matching 0
  • HiFi 0
  • preprocessing 0
  • happy 0
  • reports 0
  • notebook 0
  • bedpe 0
  • gatk4spark 0
  • mzml 0
  • somatic variants 0
  • ligate 0
  • amplicon sequences 0
  • mtDNA 0
  • windowmasker 0
  • pseudoalignment 0
  • krona chart 0
  • npz 0
  • variant_calling 0
  • mapper 0
  • typing 0
  • entrez 0
  • guide tree 0
  • covid 0
  • organelle 0
  • transcriptomics 0
  • repeat expansion 0
  • fcs-gx 0
  • chimeras 0
  • PacBio 0
  • fingerprint 0
  • PCA 0
  • miRNA 0
  • ambient RNA removal 0
  • HMM 0
  • amplicon sequencing 0
  • rna_structure 0
  • RNA 0
  • genotype-based deconvoltion 0
  • cfDNA 0
  • popscle 0
  • dna 0
  • transposons 0
  • krona 0
  • bacterial 0
  • vrhyme 0
  • untar 0
  • archiving 0
  • plink2 0
  • rsem 0
  • wastewater 0
  • transcripts 0
  • genome assembly 0
  • polishing 0
  • indel 0
  • mlst 0
  • spark 0
  • prokka 0
  • dictionary 0
  • duplication 0
  • fam 0
  • bim 0
  • insert 0
  • score 0
  • replace 0
  • pairsam 0
  • structural_variants 0
  • pan-genome 0
  • lineage 0
  • SNP 0
  • benchmarking 0
  • unzip 0
  • survivor 0
  • uncompress 0
  • fastk 0
  • pangolin 0
  • html 0
  • long_read 0
  • panel 0
  • minimap2 0
  • uLTRA 0
  • tabix 0
  • spaceranger 0
  • subsample 0
  • UMI 0
  • informative sites 0
  • kinship 0
  • identity 0
  • relatedness 0
  • lossless 0
  • small indels 0
  • observations 0
  • shapeit 0
  • scores 0
  • zip 0
  • gene expression 0
  • image_analysis 0
  • quality trimming 0
  • adapter trimming 0
  • pileup 0
  • bamtools 0
  • host 0
  • clean 0
  • bakta 0
  • mcmicro 0
  • ataqv 0
  • complement 0
  • arriba 0
  • fusion 0
  • RNA-seq 0
  • eukaryotes 0
  • prokaryotes 0
  • cut up 0
  • cool 0
  • genome mining 0
  • angsd 0
  • remove 0
  • roh 0
  • CRISPR 0
  • bracken 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
  • Duplication purging 0
  • purge duplications 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
  • intersect 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
  • mapcounter 0
  • hla_typing 0
  • maximum likelihood 0
  • hlala 0
  • hla 0
  • nacho 0
  • nanostring 0
  • mRNA 0
  • trancriptome 0
  • tama 0
  • gstama 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
  • Read depth 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
  • duplicate 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
  • 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
  • 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
  • Read coverage histogram 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
  • 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
  • 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
  • pile up 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
  • paired reads merging 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
  • GWAS 0
  • case/control 0
  • custom 0
  • associations 0
  • overlap-based merging 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
  • overlap 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
  • population genomics 0
  • postprocessing 0
  • interproscan 0
  • 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
  • overlapped bed 0
  • taxonomic assignment 0
  • svcluster 0
  • svannotate 0
  • CRISPR-Cas9 0
  • reduced 0
  • representations 0
  • splitintervals 0
  • maxbin2 0
  • maskfasta 0
  • metagenome-assembled genomes 0
  • chunking 0
  • mass-spectroscopy 0
  • splitcram 0
  • 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
  • subtract 0
  • reorder 0
  • spliced 0
  • train 0
  • adapter removal 0
  • collapsing 0
  • txt 0
  • legionella 0
  • clinical 0
  • gawk 0
  • functional genomics 0
  • variantrecalibrator 0
  • limma 0
  • Listeria monocytogenes 0
  • recalibration model 0
  • slopBed 0
  • variantfiltration 0
  • lofreq/call 0
  • lofreq/filter 0
  • qualities 0
  • AMP 0
  • peptide prediction 0
  • bases 0
  • prophage 0
  • illumina datasets 0
  • annotations 0
  • protein coding genes 0
  • VQSR 0
  • variant recalibration 0
  • virulent 0
  • subseq 0
  • grep 0
  • sequence headers 0
  • polymorphic sites 0
  • sertotype 0
  • topology 0
  • interleave 0
  • temperate 0
  • header 0
  • applyvarcal 0
  • seq 0
  • cmseq 0
  • selection 0
  • random draw 0
  • pseudohaploid 0
  • pseudodiploid 0
  • freqsum 0
  • annotateintervals 0
  • bam2seqz 0
  • gc_wiggle 0
  • induce 0
  • targets 0
  • variant quality score recalibration 0
  • bacphlip 0
  • genetic sex 0
  • antibody capture 0
  • amplicon 0
  • ampliconclip 0
  • calibratedragstrmodel 0
  • calmd 0
  • getpileupsummaries 0
  • cross-samplecontamination 0
  • faidx 0
  • calculatecontamination 0
  • insert size 0
  • repair 0
  • paired 0
  • read pairs 0
  • readgroup 0
  • assembly-binning 0
  • bedtointervallist 0
  • asereadcounter 0
  • antigen capture 0
  • scramble 0
  • cluster analysis 0
  • clusteridentifier 0
  • peak-caller 0
  • cut&tag 0
  • cut&run 0
  • chromatin 0
  • seacr 0
  • vqsr 0
  • sex determination 0
  • relative coverage 0
  • sambamba 0
  • ribosomal RNA 0
  • UShER 0
  • dbnsfp 0
  • predictions 0
  • bootstrapping 0
  • SNPs 0
  • invariant 0
  • constant 0
  • cycif 0
  • background 0
  • single-stranded 0
  • ancientDNA 0
  • rRNA 0
  • export 0
  • gene-calling 0
  • authentict 0
  • haplotype resolution 0
  • signatures 0
  • hash sketch 0
  • fracminhash sketch 0
  • read group 0
  • Haemophilus influenzae 0
  • bacterial variant calling 0
  • spatype 0
  • spa 0
  • streptococcus 0
  • sccmec 0
  • gamma 0
  • multiomics 0
  • compartments 0
  • boxplot 0
  • lifestyle 0
  • domains 0
  • rare variants 0
  • error 0
  • heattree 0
  • de-novo 0
  • longread 0
  • sha256 0
  • 256 bit 0
  • access 0
  • shinyngs 0
  • exploratory 0
  • density 0
  • dist 0
  • features 0
  • antitarget 0
  • sliding window 0
  • gangstr 0
  • autofluorescence 0
  • CRAM 0
  • SMN1 0
  • SMN2 0
  • POA 0
  • sniffles 0
  • core 0
  • snippy 0
  • duplicate marking 0
  • flagstat 0
  • phylogenetic composition 0
  • variant genetic 0
  • subset 0
  • splice 0
  • indep 0
  • gget 0
  • indep pairwise 0
  • recode 0
  • whole genome association 0
  • filterintervals 0
  • identifiers 0
  • scoring 0
  • estimatelibrarycomplexity 0
  • pmdtools 0
  • variant identifiers 0
  • porechop_abi 0
  • duplication metrics 0
  • microscopy 0
  • determinegermlinecontigploidy 0
  • gccounter 0
  • background_correction 0
  • contact 0
  • pretext 0
  • jpg 0
  • bmp 0
  • contact maps 0
  • gene finding 0
  • filtervarianttranches 0
  • exclude 0
  • element 0
  • tandem duplications 0
  • csi 0
  • genomicsdb 0
  • gatherbqsrreports 0
  • tranche filtering 0
  • hybrid-selection 0
  • mate-pair 0
  • liftovervcf 0
  • pcr 0
  • picard/renamesampleinvcf 0
  • sortvcf 0
  • deletions 0
  • insertions 0
  • CoPRO 0
  • clumping fastqs 0
  • GRO-cap 0
  • PRO-cap 0
  • CAGE 0
  • NETCAGE 0
  • RAMPAGE 0
  • csRNA-seq 0
  • STRIPE-seq 0
  • PRO-seq 0
  • GRO-seq 0
  • genetic 0
  • deduping 0
  • smaller fastqs 0
  • illumiation_correction 0
  • intervals coverage 0
  • multimapper 0
  • mapping-based 0
  • short variant discovery 0
  • bamstat 0
  • bamtools/convert 0
  • strandedness 0
  • experiment 0
  • read_pairs 0
  • fragment_size 0
  • inner_distance 0
  • combinegvcfs 0
  • read distribution 0
  • polymorphic 0
  • sequence-based 0
  • mouse 0
  • composestrtablefile 0
  • integrity 0
  • rtg 0
  • collectsvevidence 0
  • pedfilter 0
  • rocplot 0
  • collectreadcounts 0
  • rtg-tools 0
  • cnnscorevariants 0
  • salsa 0
  • salsa2 0
  • LCA 0
  • Ancestor 0
  • R 0
  • rhocall 0
  • trimBam 0
  • polymut 0
  • bamUtil 0
  • calder2 0
  • genomic intervals 0
  • normal database 0
  • panel of normals 0
  • cutoff 0
  • createsomaticpanelofnormals 0
  • haplotype purging 0
  • duplicate purging 0
  • false duplications 0
  • assembly curation 0
  • Haplotype purging 0
  • False duplications 0
  • long uncorrected reads 0
  • Assembly curation 0
  • createsequencedictionary 0
  • track 0
  • purging 0
  • bamtools/split 0
  • yaml 0
  • quast 0
  • low coverage 0
  • condensedepthevidence 0
  • dragstr 0
  • neighbour-joining 0
  • subsampling 0
  • mzML 0

Demultiplex Illumina BCL files

012

fastq fastq_idx undetermined undetermined_idx reports stats interop versions

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.

Module to build the VDJ reference needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkvdjref command.

0000

reference versions

cellranger:

Cell Ranger processes data from 10X Genomics Chromium kits. cellranger vdj takes FASTQ files from cellranger mkfastq or bcl2fastq for V(D)J libraries and performs sequence assembly and paired clonotype calling. It uses the Chromium cellular barcodes and UMIs to assemble V(D)J transcripts per cell. Clonotypes and CDR3 sequences are output as a .vloupe file which can be loaded into Loupe V(D)J Browser.

Module to use Cell Ranger's pipelines analyze sequencing data produced from Chromium Single Cell Immune Profiling.

010

outs versions

cellranger:

Cell Ranger processes data from 10X Genomics Chromium kits. cellranger vdj takes FASTQ files from cellranger mkfastq or bcl2fastq for V(D)J libraries and performs sequence assembly and paired clonotype calling. It uses the Chromium cellular barcodes and UMIs to assemble V(D)J transcripts per cell. Clonotypes and CDR3 sequences are output as a .vloupe file which can be loaded into Loupe V(D)J Browser.

Module to create fastqs needed by the 10x Genomics Cell Ranger Arc tool. Uses the cellranger-arc mkfastq command.

00

versions fastq

cellrangerarc:

Cell Ranger Arc 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.

Module to create fastqs needed by the 10x Genomics Cell Ranger ATAC tool. Uses the cellranger-atac mkfastq command.

00

versions fastq

cellranger-atac:

Cell Ranger ATAC 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.

Module to validate illuminaยฎ Sample Sheet v2 files.

010

samplesheet versions

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