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
  • sort 0
  • sam 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
  • classification 0
  • nanopore 0
  • quality control 0
  • classify 0
  • gtf 0
  • download 0
  • cnv 0
  • split 0
  • MSA 0
  • variant 0
  • k-mer 0
  • gfa 0
  • taxonomy 0
  • contamination 0
  • taxonomic profiling 0
  • sentieon 0
  • pacbio 0
  • somatic 0
  • convert 0
  • conversion 0
  • proteomics 0
  • count 0
  • quality 0
  • clustering 0
  • binning 0
  • VCF 0
  • copy number 0
  • ancient DNA 0
  • phylogeny 0
  • trimming 0
  • contigs 0
  • imputation 0
  • bedtools 0
  • kmer 0
  • reporting 0
  • sv 0
  • variation graph 0
  • graph 0
  • bisulfite 0
  • long reads 0
  • isoseq 0
  • bcftools 0
  • gvcf 0
  • mags 0
  • build 0
  • protein 0
  • indexing 0
  • compression 0
  • rnaseq 0
  • cna 0
  • long-read 0
  • table 0
  • picard 0
  • bisulphite 0
  • wgs 0
  • bqsr 0
  • consensus 0
  • QC 0
  • databases 0
  • methylseq 0
  • methylation 0
  • phage 0
  • depth 0
  • sequences 0
  • 5mC 0
  • openms 0
  • stats 0
  • metrics 0
  • taxonomic classification 0
  • serotype 0
  • imaging 0
  • antimicrobial resistance 0
  • visualisation 0
  • mapping 0
  • tsv 0
  • matrix 0
  • haplotype 0
  • amr 0
  • pairs 0
  • DNA methylation 0
  • WGBS 0
  • pangenome graph 0
  • markduplicates 0
  • protein sequence 0
  • searching 0
  • cluster 0
  • scWGBS 0
  • histogram 0
  • expression 0
  • neural network 0
  • aDNA 0
  • plot 0
  • structure 0
  • base quality score recalibration 0
  • bins 0
  • virus 0
  • aligner 0
  • machine learning 0
  • bisulfite sequencing 0
  • LAST 0
  • cooler 0
  • gzip 0
  • transcript 0
  • mmseqs2 0
  • damage 0
  • samtools 0
  • validation 0
  • iCLIP 0
  • low-coverage 0
  • completeness 0
  • bcf 0
  • genotype 0
  • db 0
  • bwa 0
  • biscuit 0
  • checkm 0
  • annotate 0
  • mappability 0
  • filtering 0
  • palaeogenomics 0
  • repeat 0
  • metagenome 0
  • archaeogenomics 0
  • ucsc 0
  • phasing 0
  • kraken2 0
  • example 0
  • umi 0
  • transcriptome 0
  • blast 0
  • hmmsearch 0
  • bismark 0
  • sequence 0
  • glimpse 0
  • newick 0
  • complexity 0
  • mag 0
  • gene 0
  • seqkit 0
  • gff3 0
  • peaks 0
  • germline 0
  • dedup 0
  • population genetics 0
  • decompression 0
  • spatial 0
  • evaluation 0
  • mkref 0
  • segmentation 0
  • genotyping 0
  • ncbi 0
  • msa 0
  • differential 0
  • feature 0
  • mitochondria 0
  • snp 0
  • json 0
  • prokaryote 0
  • demultiplexing 0
  • prediction 0
  • NCBI 0
  • bedGraph 0
  • plasmid 0
  • multiple sequence alignment 0
  • kmers 0
  • low frequency variant calling 0
  • scRNA-seq 0
  • cnvkit 0
  • hmmer 0
  • splicing 0
  • single 0
  • tumor-only 0
  • mirna 0
  • report 0
  • pangenome 0
  • vsearch 0
  • short-read 0
  • antimicrobial resistance genes 0
  • deduplication 0
  • duplicates 0
  • antimicrobial peptides 0
  • call 0
  • profile 0
  • 3-letter genome 0
  • amps 0
  • isolates 0
  • adapters 0
  • de novo 0
  • FASTQ 0
  • arg 0
  • merging 0
  • fragment 0
  • single cell 0
  • mem 0
  • tabular 0
  • cat 0
  • csv 0
  • text 0
  • concatenate 0
  • sourmash 0
  • summary 0
  • structural 0
  • de novo assembly 0
  • benchmark 0
  • mutect2 0
  • antibiotic resistance 0
  • counts 0
  • diversity 0
  • query 0
  • mpileup 0
  • profiling 0
  • interval 0
  • indels 0
  • wxs 0
  • microbiome 0
  • deamination 0
  • riboseq 0
  • extract 0
  • detection 0
  • MAF 0
  • coptr 0
  • clipping 0
  • visualization 0
  • ptr 0
  • view 0
  • gridss 0
  • idXML 0
  • kallisto 0
  • svtk 0
  • paf 0
  • cut 0
  • telomere 0
  • enrichment 0
  • compare 0
  • reference-free 0
  • retrotransposon 0
  • HiFi 0
  • happy 0
  • bgzip 0
  • containment 0
  • read depth 0
  • reads 0
  • hmmcopy 0
  • redundancy 0
  • bedpe 0
  • ccs 0
  • logratio 0
  • isomir 0
  • fastx 0
  • propr 0
  • preprocessing 0
  • CLIP 0
  • microsatellite 0
  • bedgraph 0
  • peak-calling 0
  • phylogenetic placement 0
  • DNA sequencing 0
  • genome assembler 0
  • fgbio 0
  • targeted sequencing 0
  • hybrid capture sequencing 0
  • STR 0
  • public datasets 0
  • sequencing 0
  • transcriptomics 0
  • SV 0
  • mtDNA 0
  • copy number alteration calling 0
  • bin 0
  • snps 0
  • bigwig 0
  • ganon 0
  • deep learning 0
  • ranking 0
  • gsea 0
  • hic 0
  • ngscheckmate 0
  • matching 0
  • compress 0
  • genmod 0
  • diamond 0
  • sample 0
  • family 0
  • haplotypecaller 0
  • miscoding lesions 0
  • palaeogenetics 0
  • umitools 0
  • archaeogenetics 0
  • interval_list 0
  • ont 0
  • circrna 0
  • quantification 0
  • ampir 0
  • BGC 0
  • pypgx 0
  • image 0
  • add 0
  • sketch 0
  • ancestry 0
  • union 0
  • abundance 0
  • fungi 0
  • DNA sequence 0
  • microarray 0
  • chunk 0
  • resistance 0
  • ATAC-seq 0
  • xeniumranger 0
  • parsing 0
  • normalization 0
  • malt 0
  • biosynthetic gene cluster 0
  • quality trimming 0
  • SNP 0
  • benchmarking 0
  • neubi 0
  • amplify 0
  • bamtools 0
  • repeat expansion 0
  • pileup 0
  • transposons 0
  • structural_variants 0
  • lossless 0
  • virulence 0
  • amplicon sequences 0
  • genome mining 0
  • duplication 0
  • spaceranger 0
  • uncompress 0
  • fcs-gx 0
  • ligate 0
  • host 0
  • chromosome 0
  • rna 0
  • PCA 0
  • clean 0
  • pangolin 0
  • scores 0
  • lineage 0
  • prokka 0
  • fingerprint 0
  • DRAMP 0
  • mzml 0
  • checkv 0
  • combine 0
  • comparisons 0
  • observations 0
  • wastewater 0
  • zip 0
  • unzip 0
  • variant_calling 0
  • bacterial 0
  • subsample 0
  • fai 0
  • covid 0
  • macrel 0
  • minimap2 0
  • uLTRA 0
  • insert 0
  • converter 0
  • fastk 0
  • roh 0
  • identity 0
  • score 0
  • relatedness 0
  • mapper 0
  • kinship 0
  • html 0
  • replace 0
  • chip-seq 0
  • adapter trimming 0
  • informative sites 0
  • small indels 0
  • long_read 0
  • ataqv 0
  • windowmasker 0
  • transcripts 0
  • png 0
  • fusion 0
  • untar 0
  • typing 0
  • rna_structure 0
  • RNA 0
  • arriba 0
  • entrez 0
  • amplicon sequencing 0
  • wig 0
  • rsem 0
  • angsd 0
  • panel 0
  • genome assembly 0
  • intervals 0
  • distance 0
  • krona 0
  • bakta 0
  • chimeras 0
  • genomes 0
  • dump 0
  • gatk4spark 0
  • pseudoalignment 0
  • nucleotide 0
  • cool 0
  • remove 0
  • RNA-seq 0
  • eukaryotes 0
  • dictionary 0
  • cut up 0
  • shapeit 0
  • ambient RNA removal 0
  • atac-seq 0
  • CRISPR 0
  • hi-c 0
  • npz 0
  • fam 0
  • dna 0
  • guide tree 0
  • cfDNA 0
  • somatic variants 0
  • microbes 0
  • miRNA 0
  • kraken 0
  • sylph 0
  • notebook 0
  • reports 0
  • gene expression 0
  • HMM 0
  • genotype-based deconvoltion 0
  • krona chart 0
  • popscle 0
  • organelle 0
  • survivor 0
  • vrhyme 0
  • bim 0
  • image_analysis 0
  • spark 0
  • das_tool 0
  • aln 0
  • C to T 0
  • mcmicro 0
  • das tool 0
  • plink2 0
  • bracken 0
  • indel 0
  • polishing 0
  • archiving 0
  • pairsam 0
  • deeparg 0
  • pan-genome 0
  • UMI 0
  • prokaryotes 0
  • bwameth 0
  • tabix 0
  • prefetch 0
  • highly_multiplexed_imaging 0
  • PacBio 0
  • mlst 0
  • complement 0
  • orf 0
  • bfiles 0
  • cnvnator 0
  • otu tables 0
  • authentication 0
  • joint genotyping 0
  • gatk 0
  • standardise 0
  • standardisation 0
  • concat 0
  • genetics 0
  • taxonomic profile 0
  • multiallelic 0
  • baf 0
  • serogroup 0
  • taxon tables 0
  • barcode 0
  • MaltExtract 0
  • variant pruning 0
  • primer 0
  • aggregate 0
  • metamaps 0
  • comparison 0
  • lift 0
  • HOPS 0
  • nucleotides 0
  • demultiplexed reads 0
  • pair 0
  • small variants 0
  • standardization 0
  • leviosam2 0
  • profiles 0
  • gene set 0
  • gem 0
  • nextclade 0
  • hidden Markov model 0
  • reformat 0
  • mask 0
  • corrupted 0
  • bustools 0
  • mapcounter 0
  • hla_typing 0
  • vcflib 0
  • hlala 0
  • hla 0
  • khmer 0
  • split_kmers 0
  • haplogroups 0
  • screen 0
  • ichorcna 0
  • xz 0
  • iphop 0
  • polyA_tail 0
  • nanostring 0
  • refine 0
  • reformatting 0
  • vg 0
  • maximum likelihood 0
  • nacho 0
  • mudskipper 0
  • instrain 0
  • orthology 0
  • parallelized 0
  • graph layout 0
  • mRNA 0
  • transcriptomic 0
  • tnhaplotyper2 0
  • archive 0
  • read-group 0
  • ped 0
  • concordance 0
  • kma 0
  • trim 0
  • screening 0
  • krakentools 0
  • rgfa 0
  • edit distance 0
  • phase 0
  • ChIP-seq 0
  • salmon 0
  • krakenuniq 0
  • interactive 0
  • genomad 0
  • microscopy 0
  • cleaning 0
  • long terminal retrotransposon 0
  • COBS 0
  • trancriptome 0
  • k-mer index 0
  • bloom filter 0
  • GPU-accelerated 0
  • xenograft 0
  • pharokka 0
  • function 0
  • tama 0
  • long terminal repeat 0
  • removal 0
  • gstama 0
  • graft 0
  • trgt 0
  • lofreq 0
  • gene set analysis 0
  • retrotransposons 0
  • gene labels 0
  • hlala_typing 0
  • functional analysis 0
  • BAM 0
  • shigella 0
  • regions 0
  • antibiotics 0
  • bam2fq 0
  • spatial_omics 0
  • random forest 0
  • metagenomes 0
  • blastn 0
  • heatmap 0
  • collate 0
  • dict 0
  • sequence analysis 0
  • long-read sequencing 0
  • proteome 0
  • structural-variant calling 0
  • dereplicate 0
  • frame-shift correction 0
  • checksum 0
  • RiPP 0
  • fasterq-dump 0
  • eido 0
  • minhash 0
  • eigenstrat 0
  • homoploymer 0
  • svdb 0
  • validate 0
  • format 0
  • rtgtools 0
  • tree 0
  • awk 0
  • image_processing 0
  • scaffolding 0
  • blastp 0
  • pharmacogenetics 0
  • deseq2 0
  • rna-seq 0
  • NRPS 0
  • rename 0
  • fixmate 0
  • sra-tools 0
  • mash 0
  • SimpleAF 0
  • mirdeep2 0
  • RNA sequencing 0
  • cvnkit 0
  • smrnaseq 0
  • estimation 0
  • antismash 0
  • single cells 0
  • spatial_transcriptomics 0
  • sequenzautils 0
  • recombination 0
  • genome bins 0
  • salmonella 0
  • eCLIP 0
  • resolve_bioscience 0
  • seqtk 0
  • parse 0
  • transformation 0
  • CNV 0
  • varcal 0
  • settings 0
  • Streptococcus pneumoniae 0
  • switch 0
  • gwas 0
  • megan 0
  • correction 0
  • find 0
  • soft-clipped clusters 0
  • ancient dna 0
  • repeats 0
  • fusions 0
  • cnv calling 0
  • Pharmacogenetics 0
  • ome-tif 0
  • GC content 0
  • MCMICRO 0
  • pigz 0
  • calling 0
  • doublets 0
  • registration 0
  • junctions 0
  • variation 0
  • RNA-Seq 0
  • micro-satellite-scan 0
  • realignment 0
  • tumor 0
  • normalize 0
  • norm 0
  • microbial 0
  • de novo assembler 0
  • simulate 0
  • deconvolution 0
  • bayesian 0
  • small genome 0
  • scatter 0
  • effect prediction 0
  • amptransformer 0
  • reheader 0
  • msisensor-pro 0
  • differential expression 0
  • merge mate pairs 0
  • regression 0
  • import 0
  • tbi 0
  • panelofnormals 0
  • evidence 0
  • adapter 0
  • interactions 0
  • intersect 0
  • taxids 0
  • allele-specific 0
  • taxon name 0
  • zlib 0
  • filtermutectcalls 0
  • proportionality 0
  • preseq 0
  • library 0
  • interval list 0
  • artic 0
  • purge duplications 0
  • ampgram 0
  • secondary metabolites 0
  • join 0
  • scaffold 0
  • reads merging 0
  • identifier 0
  • polish 0
  • instability 0
  • mitochondrion 0
  • expansionhunterdenovo 0
  • repeat_expansions 0
  • runs_of_homozygosity 0
  • metadata 0
  • allele 0
  • anndata 0
  • intersection 0
  • tab 0
  • MSI 0
  • windows 0
  • cancer genomics 0
  • emboss 0
  • snpsift 0
  • snpeff 0
  • contig 0
  • metagenomic 0
  • GEO 0
  • Read depth 0
  • fetch 0
  • unaligned 0
  • Duplication purging 0
  • UMIs 0
  • FracMinHash sketch 0
  • duplex 0
  • duplicate 0
  • signature 0
  • short reads 0
  • msi 0
  • linkbins 0
  • pangenome-scale 0
  • vsearch/sort 0
  • whamg 0
  • wavefront 0
  • long read alignment 0
  • gender determination 0
  • geo 0
  • all versus all 0
  • copy-number 0
  • yahs 0
  • mashmap 0
  • wham 0
  • copy number analysis 0
  • copy number alterations 0
  • graph projection to vcf 0
  • copy number variation 0
  • usearch 0
  • extractunbinned 0
  • sintax 0
  • rdtest2vcf 0
  • fix 0
  • predictions 0
  • CRAM 0
  • SMN1 0
  • SMN2 0
  • POA 0
  • sniffles 0
  • core 0
  • snippy 0
  • dist 0
  • dbnsfp 0
  • prepare 0
  • SNPs 0
  • features 0
  • invariant 0
  • constant 0
  • rRNA 0
  • ribosomal RNA 0
  • signatures 0
  • hash sketch 0
  • fracminhash sketch 0
  • spatype 0
  • spa 0
  • streptococcus 0
  • sccmec 0
  • sliding window 0
  • density 0
  • catpack 0
  • sex determination 0
  • 16S 0
  • selection 0
  • random draw 0
  • pseudohaploid 0
  • pseudodiploid 0
  • CRISPRi 0
  • freqsum 0
  • bam2seqz 0
  • gc_wiggle 0
  • induce 0
  • genetic sex 0
  • boxplot 0
  • relative coverage 0
  • taxonomic composition 0
  • rare variants 0
  • error 0
  • de-novo 0
  • longread 0
  • sha256 0
  • 256 bit 0
  • mzML 0
  • shinyngs 0
  • exploratory 0
  • variantcalling 0
  • Computational Immunology 0
  • paired reads re-pairing 0
  • regex 0
  • scRNA-Seq 0
  • files 0
  • patterns 0
  • upd 0
  • uniparental 0
  • disomy 0
  • snv 0
  • downsample 0
  • downsample bam 0
  • subsample bam 0
  • vcf2db 0
  • doublet 0
  • gemini 0
  • maf 0
  • lua 0
  • toml 0
  • vcfbreakmulti 0
  • uniq 0
  • deduplicate 0
  • VCFtools 0
  • verifybamid 0
  • DNA contamination estimation 0
  • construct 0
  • umicollapse 0
  • ucsc/liftover 0
  • Bioinformatics Tools 0
  • fast5 0
  • detecting svs 0
  • short-read sequencing 0
  • Immune Deconvolution 0
  • svtk/baftest 0
  • baftest 0
  • countsvtypes 0
  • rdtest 0
  • vcf2bed 0
  • decompress 0
  • polya tail 0
  • Mycobacterium tuberculosis 0
  • gtftogenepred 0
  • chromosomal rearrangements 0
  • eucaryotes 0
  • coding 0
  • cds 0
  • transcroder 0
  • sequencing adapters 0
  • bedgraphtobigwig 0
  • bigbed 0
  • bedtobigbed 0
  • genepred 0
  • refflat 0
  • mapad 0
  • telseq 0
  • adna 0
  • guidetree 0
  • droplet based single cells 0
  • cell segmentation 0
  • lexogen 0
  • genotype-based demultiplexing 0
  • donor deconvolution 0
  • cellsnp 0
  • trimfq 0
  • vcflib/vcffixup 0
  • nuclear segmentation 0
  • import segmentation 0
  • solo 0
  • AC/NS/AF 0
  • Pacbio 0
  • scvi 0
  • InterProScan 0
  • bwamem2 0
  • bwameme 0
  • grabix 0
  • ribosomal 0
  • 10x 0
  • p-value 0
  • significance statistic 0
  • logFC 0
  • subsetting 0
  • regulatory network 0
  • transcription factors 0
  • paraphase 0
  • selector 0
  • cram-size 0
  • busco 0
  • MMseqs2 0
  • size 0
  • rna velocity 0
  • spatial_neighborhoods 0
  • scimap 0
  • Bayesian 0
  • structural-variants 0
  • omics 0
  • biological activity 0
  • prior knowledge 0
  • tag 0
  • cell_barcodes 0
  • mygene 0
  • go 0
  • pile up 0
  • nanopore sequencing 0
  • seq 0
  • retrieval 0
  • extension 0
  • grea 0
  • functional enrichment 0
  • relabel 0
  • translation 0
  • paired reads merging 0
  • overlap-based merging 0
  • check 0
  • hamming-distance 0
  • hashing-based deconvoltion 0
  • gnu 0
  • coreutils 0
  • generic 0
  • transposable element 0
  • barcodes 0
  • quality check 0
  • case/control 0
  • haplotag 0
  • impute-info 0
  • tags 0
  • translate 0
  • tag2tag 0
  • hashing-based deconvolution 0
  • rank 0
  • java 0
  • script 0
  • jvarkit 0
  • xml 0
  • svg 0
  • setgt 0
  • standard 0
  • staging 0
  • functional 0
  • ATACshift 0
  • Staging 0
  • shift 0
  • ATACseq 0
  • fastqfilter 0
  • microRNA 0
  • multiqc 0
  • mass_error 0
  • search engine 0
  • vsearch/fastqfilter 0
  • vsearch/dereplicate 0
  • poolseq 0
  • variant-calling 0
  • stardist 0
  • tar 0
  • tarball 0
  • doublet_detection 0
  • cgMLST 0
  • realign 0
  • quality_control 0
  • emoji 0
  • circular 0
  • spot 0
  • orthogroup 0
  • orthologs 0
  • source tracking 0
  • sage 0
  • mass spectrometry 0
  • featuretable 0
  • extraction 0
  • controlstatistics 0
  • WGS 0
  • targz 0
  • elprep 0
  • elfasta 0
  • nucleotide content 0
  • redundant 0
  • nanoq 0
  • Read filters 0
  • AT content 0
  • Read trimming 0
  • nucBed 0
  • Read report 0
  • drug categorization 0
  • uniques 0
  • Illumina 0
  • associations 0
  • GWAS 0
  • c to t 0
  • peak picking 0
  • transmembrane 0
  • updatedata 0
  • genome graph 0
  • tnseq 0
  • run 0
  • decoy 0
  • pdb 0
  • htseq 0
  • rrna 0
  • block substitutions 0
  • decomposeblocksub 0
  • sompy 0
  • identity-by-descent 0
  • site frequency spectrum 0
  • hmmfetch 0
  • ancestral alleles 0
  • derived alleles 0
  • tnfilter 0
  • array_cgh 0
  • cytosure 0
  • vector 0
  • gprofiler2 0
  • gost 0
  • rad 0
  • mgi 0
  • recovery 0
  • structural variant 0
  • bam2fastx 0
  • bam2fastq 0
  • decompose 0
  • simulation 0
  • airrseq 0
  • dnamodelapply 0
  • proteus 0
  • readproteingroups 0
  • eigenvectors 0
  • hicPCA 0
  • sliding 0
  • malformed 0
  • snakemake 0
  • workflow 0
  • workflow_mode 0
  • createreadcountpanelofnormals 0
  • copyratios 0
  • denoisereadcounts 0
  • readwriter 0
  • dnascope 0
  • reverse complement 0
  • partitioning 0
  • chip 0
  • groupby 0
  • tnscope 0
  • bgen 0
  • chloroplast 0
  • confidence 0
  • blat 0
  • alr 0
  • clr 0
  • boxcox 0
  • Escherichia coli 0
  • propd 0
  • Read coverage histogram 0
  • immcantation 0
  • immunoinformatics 0
  • association 0
  • hardy-weinberg 0
  • r 0
  • coexpression 0
  • correlation 0
  • corpcor 0
  • assay 0
  • phylogenetics 0
  • minimum_evolution 0
  • distance-based 0
  • nucleotide sequence 0
  • homologs 0
  • multi-tool 0
  • predict 0
  • morphology 0
  • hwe statistics 0
  • hostile 0
  • hwe equilibrium 0
  • reference-independent 0
  • genotype likelihood 0
  • collapse 0
  • liftover 0
  • probabilistic realignment 0
  • seqfu 0
  • n50 0
  • resegment 0
  • cell_type_identification 0
  • cell_phenotyping 0
  • machine_learning 0
  • clahe 0
  • refresh 0
  • python 0
  • quarto 0
  • co-orthology 0
  • install 0
  • homology 0
  • leafcutter 0
  • sequence similarity 0
  • spectral clustering 0
  • comparative genomics 0
  • deep variant 0
  • mutect 0
  • idx 0
  • regtools 0
  • plotting 0
  • transform 0
  • gaps 0
  • introns 0
  • joint-genotyping 0
  • standardize 0
  • genotypegvcf 0
  • scanpy 0
  • parallel 0
  • plastid 0
  • resfinder 0
  • resistance genes 0
  • raw 0
  • mgf 0
  • parquet 0
  • metagenome assembler 0
  • human removal 0
  • decontamination 0
  • parser 0
  • dbsnp 0
  • cobra 0
  • taxonomic assignment 0
  • header 0
  • vqsr 0
  • rust 0
  • variant caller 0
  • somatic variant calling 0
  • germline variant calling 0
  • bacterial variant calling 0
  • bootstrapping 0
  • UShER 0
  • gamma 0
  • gene-calling 0
  • gangstr 0
  • heattree 0
  • targets 0
  • annotateintervals 0
  • variant quality score recalibration 0
  • asereadcounter 0
  • lint 0
  • bedtointervallist 0
  • calculatecontamination 0
  • cross-samplecontamination 0
  • getpileupsummaries 0
  • calibratedragstrmodel 0
  • cnnscorevariants 0
  • collectreadcounts 0
  • collectsvevidence 0
  • combinegvcfs 0
  • short variant discovery 0
  • composestrtablefile 0
  • dragstr 0
  • condensedepthevidence 0
  • createsequencedictionary 0
  • fq 0
  • random 0
  • determinegermlinecontigploidy 0
  • percent on target 0
  • escherichia coli 0
  • PEP 0
  • schema 0
  • pep 0
  • eigenstratdatabasetools 0
  • eklipse 0
  • circos 0
  • deletion 0
  • split by chromosome 0
  • embl 0
  • genbank 0
  • swissprot 0
  • Streptococcus pyogenes 0
  • endogenous DNA 0
  • cache 0
  • generate 0
  • consensus sequence 0
  • single molecule 0
  • zipperbams 0
  • ubam 0
  • unmapped 0
  • groupreads 0
  • duplexumi 0
  • public 0
  • str 0
  • ENA 0
  • SRA 0
  • ANI 0
  • ARGs 0
  • antibiotic resistance genes 0
  • faqcs 0
  • createsomaticpanelofnormals 0
  • duplication metrics 0
  • structural variation 0
  • Mykrobe 0
  • variantfiltration 0
  • recalibration model 0
  • variantrecalibrator 0
  • gawk 0
  • txt 0
  • file parsing 0
  • bgc 0
  • genome profile 0
  • compound 0
  • models 0
  • genome size 0
  • genome heterozygosity 0
  • repeat content 0
  • Salmonella Typhi 0
  • gfastats 0
  • svannotate 0
  • genome summary 0
  • genome manipulation 0
  • genome statistics 0
  • gget 0
  • low coverage 0
  • Sample 0
  • Haplotypes 0
  • Imputation 0
  • joint-variant-calling 0
  • GNU 0
  • merge compare 0
  • genomes on a tree 0
  • tama_collapse.py 0
  • gene model 0
  • svcluster 0
  • splitintervals 0
  • estimatelibrarycomplexity 0
  • learnreadorientationmodel 0
  • filterintervals 0
  • filtervarianttranches 0
  • tranche filtering 0
  • gatherbqsrreports 0
  • genomicsdb 0
  • genomicsdbimport 0
  • jointgenotyping 0
  • panelofnormalscreation 0
  • germline contig ploidy 0
  • germlinecnvcaller 0
  • germlinevariantsites 0
  • getpileupsumaries 0
  • readcountssummary 0
  • indexfeaturefile 0
  • readorientationartifacts 0
  • splitcram 0
  • reblockgvcf 0
  • site depth 0
  • shiftintervals 0
  • shiftfasta 0
  • shiftchain 0
  • selectvariants 0
  • revert 0
  • printsvevidence 0
  • leftalignandtrimvariants 0
  • printreads 0
  • preprocessintervals 0
  • postprocessgermlinecnvcalls 0
  • snvs 0
  • mutectstats 0
  • mergebamalignment 0
  • depth information 0
  • duphold 0
  • gstama/merge 0
  • BCF 0
  • bacphlip 0
  • mouse 0
  • bamtools/convert 0
  • yaml 0
  • bamtools/split 0
  • bamUtil 0
  • trimBam 0
  • element 0
  • illumiation_correction 0
  • background_correction 0
  • clumping fastqs 0
  • smaller fastqs 0
  • deduping 0
  • csi 0
  • update header 0
  • temperate 0
  • biallelic 0
  • homozygosity 0
  • autozygosity 0
  • sorting 0
  • bamtobed 0
  • closest 0
  • genomecov 0
  • getfasta 0
  • overlap 0
  • jaccard 0
  • chunking 0
  • maskfasta 0
  • overlapped bed 0
  • multinterval 0
  • virulent 0
  • lifestyle 0
  • region 0
  • doCounts 0
  • contiguate 0
  • antimicrobial reistance 0
  • adapterremoval 0
  • admixture 0
  • reference panels 0
  • affy 0
  • Staphylococcus aureus 0
  • amp 0
  • antimicrobial peptide prediction 0
  • AMPs 0
  • model 0
  • post Post-processing 0
  • nuclear contamination estimate 0
  • allele counts 0
  • installation 0
  • autofluorescence 0
  • bias 0
  • cycif 0
  • background 0
  • single-stranded 0
  • ancientDNA 0
  • authentict 0
  • read group 0
  • ATLAS 0
  • HLA 0
  • sequencing_bias 0
  • post mortem damage 0
  • atlas 0
  • mkarv 0
  • http(s) 0
  • utility 0
  • shiftBed 0
  • sizes 0
  • segment 0
  • UNet 0
  • antitarget 0
  • export 0
  • target 0
  • partition histograms 0
  • concoct 0
  • nucleotide composition 0
  • subcontigs 0
  • cooler/balance 0
  • cload 0
  • digest 0
  • enzyme 0
  • makebins 0
  • genomic bins 0
  • mcool 0
  • TMA dearray 0
  • cmseq 0
  • pcr duplicates 0
  • blastx 0
  • cumulative coverage 0
  • scatterplot 0
  • corrrelation 0
  • track 0
  • paired-end 0
  • cutesv 0
  • Segmentation 0
  • gct 0
  • cls 0
  • na 0
  • version 0
  • custom 0
  • Cores 0
  • access 0
  • protein coding genes 0
  • bases 0
  • domains 0
  • slopBed 0
  • subtract 0
  • unionBedGraphs 0
  • bioawk 0
  • file manipulation 0
  • sorted 0
  • Salmonella enterica 0
  • subtyping 0
  • tblastn 0
  • postprocessing 0
  • cadd 0
  • calder2 0
  • topology 0
  • compartments 0
  • Assembly 0
  • polymorphic sites 0
  • quality assurnce 0
  • polymorphic 0
  • polymut 0
  • splice 0
  • chromosome_visualization 0
  • duplicate removal 0
  • chromap 0
  • qa 0
  • hifi 0
  • crispr 0
  • antibody capture 0
  • antigen capture 0
  • multiomics 0
  • cellpose 0
  • TAMA 0
  • gstama/polyacleanup 0
  • interleave 0
  • GRO-seq 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
  • csRNA-seq 0
  • STRIPE-seq 0
  • PRO-seq 0
  • genetic 0
  • liftovervcf 0
  • exclude 0
  • variant identifiers 0
  • subset 0
  • indep 0
  • indep pairwise 0
  • recode 0
  • whole genome association 0
  • identifiers 0
  • scoring 0
  • variant genetic 0
  • pmdtools 0
  • porechop_abi 0
  • contact 0
  • pretext 0
  • pcr 0
  • mate-pair 0
  • bmp 0
  • select 0
  • graph formats 0
  • graph viz 0
  • tumor/normal 0
  • hla-typing 0
  • ILP 0
  • HLA-I 0
  • block-compressed 0
  • PCR/optical duplicates 0
  • flip 0
  • upper-triangular matrix 0
  • ligation junctions 0
  • pairtools 0
  • pairstools 0
  • restriction fragments 0
  • paragraph 0
  • hybrid-selection 0
  • motif 0
  • phylogenetic composition 0
  • illumina datasets 0
  • identification 0
  • prophage 0
  • phantom peaks 0
  • ChIP-Seq 0
  • pedigrees 0
  • graphs 0
  • read 0
  • pair-end 0
  • pbp 0
  • subreads 0
  • pbmerge 0
  • pbbam 0
  • jpg 0
  • contact maps 0
  • graph stats 0
  • readgroup 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
  • read pairs 0
  • scramble 0
  • salsa 0
  • applyvarcal 0
  • sertotype 0
  • sequence headers 0
  • grep 0
  • subseq 0
  • variant recalibration 0
  • VQSR 0
  • assembly-binning 0
  • cluster analysis 0
  • seacr 0
  • chromatin 0
  • cut&run 0
  • cut&tag 0
  • peak-caller 0
  • clusteridentifier 0
  • salsa2 0
  • rtg-tools 0
  • gene finding 0
  • neighbour-joining 0
  • intervals coverage 0
  • genomic intervals 0
  • normal database 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
  • purging 0
  • quast 0
  • subsampling 0
  • rocplot 0
  • inner_distance 0
  • pedfilter 0
  • rtg 0
  • integrity 0
  • mapping-based 0
  • sequence-based 0
  • read distribution 0
  • fragment_size 0
  • long uncorrected reads 0
  • read_pairs 0
  • experiment 0
  • strandedness 0
  • bamstat 0
  • R 0
  • rhocall 0
  • graph unchopping 0
  • combine graphs 0
  • GTDB taxonomy 0
  • k-mer counting 0
  • probability_maps 0
  • population genomics 0
  • interproscan 0
  • genomic islands 0
  • insertion 0
  • jasminesv 0
  • jasmine 0
  • Python 0
  • Jupyter 0
  • jupytext 0
  • papermill 0
  • kallisto/index 0
  • quant 0
  • digital normalization 0
  • effective genome size 0
  • pixel classification 0
  • Klebsiella 0
  • pneumoniae 0
  • kegg 0
  • kofamscan 0
  • combining 0
  • reorder 0
  • spliced 0
  • train 0
  • adapter removal 0
  • collapsing 0
  • legionella 0
  • clinical 0
  • pneumophila 0
  • limma 0
  • pixel_classification 0
  • multicut 0
  • lofreq/call 0
  • mitochondrial 0
  • genome taxonomy database 0
  • archaea 0
  • gunc 0
  • gunzip 0
  • gvcftools 0
  • extract_variants 0
  • extractvariants 0
  • abricate 0
  • amrfinderplus 0
  • fARGene 0
  • rgi 0
  • ibd 0
  • hbd 0
  • beagle 0
  • Haemophilus influenzae 0
  • genome browser 0
  • pos 0
  • js 0
  • igv.js 0
  • igv 0
  • IDR 0
  • panel_of_normals 0
  • haemophilus 0
  • annotations 0
  • haplotype resolution 0
  • hmtnote 0
  • Hidden Markov Model 0
  • amino acid 0
  • HMMER 0
  • readcounter 0
  • gccounter 0
  • Listeria monocytogenes 0
  • lofreq/filter 0
  • odgi 0
  • mitochondrial to nuclear ratio 0
  • methylation bias 0
  • mbias 0
  • assembler 0
  • de Bruijn 0
  • microrna 0
  • target prediction 0
  • mitochondrial genome 0
  • reference genome 0
  • mosdepth 0
  • otu table 0
  • microsatellite instability 0
  • scan 0
  • mtnucratio 0
  • ratio 0
  • bioinformatics tools 0
  • unionsum 0
  • NextGenMap 0
  • squeeze 0
  • graph drawing 0
  • graph construction 0
  • gender 0
  • Neisseria gonorrhoeae 0
  • ngm 0
  • sequencing summary 0
  • Beautiful stand-alone HTML report 0
  • mobile element insertions 0
  • somatic structural variations 0
  • cancer genome 0
  • contaminant 0
  • SNP table 0
  • GATK UnifiedGenotyper 0
  • metaphlan 0
  • ploidy 0
  • qualities 0
  • maxbin2 0
  • AMP 0
  • peptide prediction 0
  • functional genomics 0
  • sgRNA 0
  • CRISPR-Cas9 0
  • maximum-likelihood 0
  • rra 0
  • DNA damage 0
  • NGS 0
  • damage patterns 0
  • estimate 0
  • mash/sketch 0
  • reduced 0
  • representations 0
  • metagenome-assembled genomes 0
  • smudgeplot 0
  • rma6 0
  • assembly evaluation 0
  • Merqury 0
  • contour map 0
  • 3D heat map 0
  • k-mer frequency 0
  • Neisseria meningitidis 0
  • daa 0
  • mass-spectroscopy 0
  • debruijn 0
  • denovo 0
  • megahit 0
  • 128 bit 0
  • MD5 0
  • mcr-1 0
  • hhsuite 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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