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.

  • fasta 16
  • LAST 8
  • genomics 7
  • fastq 7
  • alignment 5
  • MAF 5
  • bed 4
  • annotation 4
  • blast 4
  • database 3
  • bacteria 3
  • antibiotic resistance 3
  • bam 2
  • vcf 2
  • metagenomics 2
  • sort 2
  • align 2
  • gff 2
  • nanopore 2
  • serotype 2
  • amr 2
  • gzip 2
  • repeat 2
  • plasmid 2
  • retrotransposon 2
  • sylph 2
  • find 2
  • pigz 2
  • blastn 2
  • index 1
  • reference 1
  • assembly 1
  • structural variants 1
  • variant calling 1
  • map 1
  • classification 1
  • download 1
  • split 1
  • convert 1
  • count 1
  • phylogeny 1
  • bedtools 1
  • trimming 1
  • reporting 1
  • long reads 1
  • rnaseq 1
  • databases 1
  • indexing 1
  • phage 1
  • imaging 1
  • antimicrobial resistance 1
  • sequences 1
  • markduplicates 1
  • pairs 1
  • cluster 1
  • plot 1
  • virus 1
  • bwa 1
  • gene 1
  • peaks 1
  • sketch 1
  • sequence 1
  • dedup 1
  • seqkit 1
  • duplicates 1
  • mirna 1
  • NCBI 1
  • deduplication 1
  • antimicrobial resistance genes 1
  • short-read 1
  • concatenate 1
  • cat 1
  • adapters 1
  • profile 1
  • arg 1
  • FASTQ 1
  • enrichment 1
  • telomere 1
  • DNA sequence 1
  • duplication 1
  • npz 1
  • polishing 1
  • mlst 1
  • replace 1
  • aln 1
  • quality trimming 1
  • microbes 1
  • prokaryotes 1
  • png 1
  • adapter trimming 1
  • long terminal repeat 1
  • mask 1
  • kma 1
  • pair 1
  • long terminal retrotransposon 1
  • shigella 1
  • removal 1
  • spatial_transcriptomics 1
  • resolve_bioscience 1
  • orthologs 1
  • tree 1
  • metadata 1
  • microbial 1
  • parse 1
  • fetch 1
  • identifier 1
  • GEO 1
  • Escherichia coli 1
  • resistance genes 1
  • parallel 1
  • resfinder 1
  • subtract 1
  • rrna 1
  • closest 1
  • polya tail 1
  • fast5 1
  • copy number variation 1
  • CRISPRi 1
  • orthogroup 1
  • rna velocity 1
  • retrieval 1
  • reorder 1
  • spliced 1
  • train 1
  • cancer genome 1
  • somatic structural variations 1
  • mobile element insertions 1
  • microrna 1
  • target prediction 1
  • mitochondrial genome 1
  • reference genome 1
  • amrfinderplus 1
  • spa 1
  • sequence headers 1
  • spatype 1
  • prophage 1
  • identification 1
  • PCR/optical duplicates 1
  • ligation junctions 1
  • pairtools 1
  • public 1
  • ENA 1
  • SRA 1
  • depth information 1
  • structural variation 1
  • duphold 1
  • gene finding 1
  • genome 0
  • gatk4 0
  • cram 0
  • sam 0
  • merge 0
  • filter 0
  • statistics 0
  • coverage 0
  • variants 0
  • qc 0
  • classify 0
  • quality control 0
  • gtf 0
  • cnv 0
  • MSA 0
  • taxonomy 0
  • k-mer 0
  • gfa 0
  • variant 0
  • taxonomic profiling 0
  • contamination 0
  • pacbio 0
  • sentieon 0
  • somatic 0
  • conversion 0
  • clustering 0
  • binning 0
  • proteomics 0
  • quality 0
  • single-cell 0
  • ancient DNA 0
  • copy number 0
  • VCF 0
  • imputation 0
  • contigs 0
  • mags 0
  • bisulfite 0
  • build 0
  • gvcf 0
  • bcftools 0
  • isoseq 0
  • variation graph 0
  • kmer 0
  • graph 0
  • sv 0
  • bqsr 0
  • methylation 0
  • methylseq 0
  • bisulphite 0
  • compression 0
  • long-read 0
  • illumina 0
  • table 0
  • consensus 0
  • protein 0
  • cna 0
  • picard 0
  • wgs 0
  • QC 0
  • depth 0
  • stats 0
  • visualisation 0
  • taxonomic classification 0
  • openms 0
  • metrics 0
  • 5mC 0
  • demultiplex 0
  • mapping 0
  • tsv 0
  • DNA methylation 0
  • aDNA 0
  • histogram 0
  • structure 0
  • scWGBS 0
  • WGBS 0
  • searching 0
  • protein sequence 0
  • pangenome graph 0
  • bins 0
  • base quality score recalibration 0
  • neural network 0
  • matrix 0
  • haplotype 0
  • expression 0
  • samtools 0
  • metagenome 0
  • cooler 0
  • mmseqs2 0
  • validation 0
  • aligner 0
  • low-coverage 0
  • completeness 0
  • biscuit 0
  • checkm 0
  • annotate 0
  • db 0
  • filtering 0
  • bisulfite sequencing 0
  • bcf 0
  • mappability 0
  • phasing 0
  • machine learning 0
  • transcript 0
  • iCLIP 0
  • damage 0
  • palaeogenomics 0
  • archaeogenomics 0
  • genotype 0
  • genotyping 0
  • newick 0
  • mag 0
  • decompression 0
  • bismark 0
  • umi 0
  • complexity 0
  • mkref 0
  • hmmer 0
  • segmentation 0
  • ncbi 0
  • population genetics 0
  • spatial 0
  • ucsc 0
  • evaluation 0
  • example 0
  • transcriptome 0
  • msa 0
  • glimpse 0
  • kraken2 0
  • hmmsearch 0
  • gff3 0
  • germline 0
  • prediction 0
  • mitochondria 0
  • bedGraph 0
  • prokaryote 0
  • demultiplexing 0
  • antimicrobial peptides 0
  • snp 0
  • report 0
  • feature 0
  • differential 0
  • json 0
  • tumor-only 0
  • vsearch 0
  • pangenome 0
  • single 0
  • splicing 0
  • cnvkit 0
  • kmers 0
  • scRNA-seq 0
  • multiple sequence alignment 0
  • low frequency variant calling 0
  • de novo assembly 0
  • de novo 0
  • benchmark 0
  • 3-letter genome 0
  • sourmash 0
  • view 0
  • call 0
  • query 0
  • microbiome 0
  • svtk 0
  • diversity 0
  • amps 0
  • gridss 0
  • merging 0
  • structural 0
  • riboseq 0
  • clipping 0
  • mem 0
  • summary 0
  • single cell 0
  • indels 0
  • interval 0
  • counts 0
  • profiling 0
  • distance 0
  • text 0
  • wxs 0
  • idXML 0
  • csv 0
  • isolates 0
  • visualization 0
  • detection 0
  • coptr 0
  • ptr 0
  • tabular 0
  • deamination 0
  • fragment 0
  • kallisto 0
  • mutect2 0
  • extract 0
  • mpileup 0
  • xeniumranger 0
  • compress 0
  • palaeogenetics 0
  • bgzip 0
  • fastx 0
  • gsea 0
  • miscoding lesions 0
  • BGC 0
  • CLIP 0
  • fungi 0
  • hic 0
  • deep learning 0
  • read depth 0
  • biosynthetic gene cluster 0
  • cut 0
  • compare 0
  • bin 0
  • HMM 0
  • ganon 0
  • quantification 0
  • parsing 0
  • containment 0
  • preprocessing 0
  • microarray 0
  • interval_list 0
  • ccs 0
  • haplotypecaller 0
  • hmmcopy 0
  • paf 0
  • HiFi 0
  • happy 0
  • ancestry 0
  • bedgraph 0
  • genmod 0
  • ranking 0
  • peak-calling 0
  • skani 0
  • reference-free 0
  • microsatellite 0
  • bigwig 0
  • SV 0
  • diamond 0
  • sample 0
  • sequencing 0
  • DNA sequencing 0
  • targeted sequencing 0
  • hybrid capture sequencing 0
  • copy number alteration calling 0
  • snps 0
  • mtDNA 0
  • rna 0
  • genome assembler 0
  • public datasets 0
  • phylogenetic placement 0
  • malt 0
  • STR 0
  • family 0
  • fgbio 0
  • matching 0
  • ngscheckmate 0
  • reads 0
  • ampir 0
  • circrna 0
  • archaeogenetics 0
  • ont 0
  • bcl2fastq 0
  • redundancy 0
  • ATAC-seq 0
  • image 0
  • union 0
  • normalization 0
  • pypgx 0
  • abundance 0
  • resistance 0
  • chromosome 0
  • transcriptomics 0
  • propr 0
  • logratio 0
  • umitools 0
  • isomir 0
  • add 0
  • clean 0
  • bedpe 0
  • chunk 0
  • benchmarking 0
  • plink2 0
  • pseudoalignment 0
  • variant_calling 0
  • complement 0
  • hidden Markov model 0
  • krona chart 0
  • RNA 0
  • rna_structure 0
  • fcs-gx 0
  • reports 0
  • fingerprint 0
  • bakta 0
  • PCA 0
  • prokka 0
  • notebook 0
  • rsem 0
  • dna 0
  • transposons 0
  • bacterial 0
  • cfDNA 0
  • bracken 0
  • mapper 0
  • guide tree 0
  • ataqv 0
  • indel 0
  • amplicon sequencing 0
  • ambient RNA removal 0
  • bwameth 0
  • windowmasker 0
  • typing 0
  • fam 0
  • mzml 0
  • small indels 0
  • somatic variants 0
  • fai 0
  • neubi 0
  • subsample 0
  • amplify 0
  • SNP 0
  • macrel 0
  • organelle 0
  • gatk4spark 0
  • highly_multiplexed_imaging 0
  • wastewater 0
  • spark 0
  • mcmicro 0
  • converter 0
  • image_analysis 0
  • intervals 0
  • panel 0
  • DRAMP 0
  • bim 0
  • dictionary 0
  • entrez 0
  • scores 0
  • combine 0
  • comparisons 0
  • insert 0
  • krona 0
  • wig 0
  • structural_variants 0
  • fastk 0
  • UMI 0
  • lineage 0
  • pangolin 0
  • covid 0
  • pan-genome 0
  • pairsam 0
  • repeat expansion 0
  • html 0
  • roh 0
  • virulence 0
  • amplicon sequences 0
  • vrhyme 0
  • arriba 0
  • score 0
  • cut up 0
  • genome mining 0
  • kraken 0
  • fusion 0
  • dist 0
  • cool 0
  • lossless 0
  • long_read 0
  • dump 0
  • shapeit 0
  • untar 0
  • pileup 0
  • CRISPR 0
  • gene expression 0
  • relatedness 0
  • bamtools 0
  • checkv 0
  • chip-seq 0
  • tabix 0
  • transcripts 0
  • genome assembly 0
  • atac-seq 0
  • survivor 0
  • ligate 0
  • eukaryotes 0
  • spaceranger 0
  • uLTRA 0
  • RNA-seq 0
  • informative sites 0
  • kinship 0
  • identity 0
  • minimap2 0
  • uncompress 0
  • observations 0
  • cellranger 0
  • mkfastq 0
  • angsd 0
  • genomes 0
  • hi-c 0
  • deeparg 0
  • host 0
  • das_tool 0
  • miRNA 0
  • das tool 0
  • PacBio 0
  • C to T 0
  • unzip 0
  • genotype-based deconvoltion 0
  • nucleotide 0
  • archiving 0
  • remove 0
  • zip 0
  • chimeras 0
  • prefetch 0
  • popscle 0
  • phase 0
  • minhash 0
  • genetics 0
  • hlala 0
  • mash 0
  • zlib 0
  • hla_typing 0
  • mudskipper 0
  • hla 0
  • trancriptome 0
  • tama 0
  • pharokka 0
  • metamaps 0
  • corrupted 0
  • nacho 0
  • checksum 0
  • haplotypes 0
  • transcriptomic 0
  • concordance 0
  • interactions 0
  • lofreq 0
  • mapcounter 0
  • retrotransposons 0
  • lift 0
  • salmon 0
  • hlala_typing 0
  • functional analysis 0
  • serogroup 0
  • xz 0
  • regression 0
  • bloom filter 0
  • k-mer index 0
  • krakentools 0
  • reformat 0
  • refine 0
  • maximum likelihood 0
  • nanostring 0
  • function 0
  • gstama 0
  • mRNA 0
  • taxids 0
  • taxon name 0
  • iphop 0
  • krakenuniq 0
  • haplogroups 0
  • screen 0
  • COBS 0
  • barcode 0
  • ichorcna 0
  • bustools 0
  • primer 0
  • archive 0
  • khmer 0
  • gene set analysis 0
  • polyA_tail 0
  • instrain 0
  • gene set 0
  • interactive 0
  • standardise 0
  • read-group 0
  • differential expression 0
  • vg 0
  • salmonella 0
  • varcal 0
  • fusions 0
  • soft-clipped clusters 0
  • doublets 0
  • smrnaseq 0
  • leviosam2 0
  • anndata 0
  • RNA sequencing 0
  • vcflib 0
  • mirdeep2 0
  • rename 0
  • fixmate 0
  • gene labels 0
  • dict 0
  • collate 0
  • bam2fq 0
  • scaffolding 0
  • rtgtools 0
  • hostile 0
  • junctions 0
  • decontamination 0
  • runs_of_homozygosity 0
  • seqtk 0
  • transformation 0
  • scaffold 0
  • FracMinHash sketch 0
  • standardisation 0
  • taxonomic profile 0
  • standardization 0
  • otu tables 0
  • frame-shift correction 0
  • svdb 0
  • long-read sequencing 0
  • de novo assembler 0
  • small genome 0
  • signature 0
  • taxon tables 0
  • join 0
  • sequenzautils 0
  • cancer genomics 0
  • sequence analysis 0
  • Pharmacogenetics 0
  • pharmacogenetics 0
  • snpsift 0
  • snpeff 0
  • effect prediction 0
  • switch 0
  • ancient dna 0
  • Streptococcus pneumoniae 0
  • polish 0
  • contig 0
  • megan 0
  • tumor 0
  • nucleotides 0
  • graph layout 0
  • split_kmers 0
  • multiallelic 0
  • small variants 0
  • nextclade 0
  • rgfa 0
  • msisensor-pro 0
  • tnhaplotyper2 0
  • micro-satellite-scan 0
  • msi 0
  • cnvnator 0
  • variation 0
  • instability 0
  • MSI 0
  • homoploymer 0
  • reformatting 0
  • profiles 0
  • orthology 0
  • GC content 0
  • parallelized 0
  • trgt 0
  • ampgram 0
  • SimpleAF 0
  • amptransformer 0
  • duplicate 0
  • Read depth 0
  • Duplication purging 0
  • purge duplications 0
  • MCMICRO 0
  • ome-tif 0
  • repeats 0
  • dereplicate 0
  • library 0
  • preseq 0
  • adapter 0
  • GPU-accelerated 0
  • import 0
  • variant pruning 0
  • bfiles 0
  • image_processing 0
  • registration 0
  • mitochondrion 0
  • human removal 0
  • screening 0
  • cleaning 0
  • proportionality 0
  • ped 0
  • comparison 0
  • orf 0
  • interval list 0
  • antibiotics 0
  • intersection 0
  • structural-variant calling 0
  • emboss 0
  • joint genotyping 0
  • gatk 0
  • deconvolution 0
  • bayesian 0
  • xenograft 0
  • graft 0
  • fasterq-dump 0
  • antismash 0
  • sra-tools 0
  • RNA-Seq 0
  • settings 0
  • version 0
  • NRPS 0
  • secondary metabolites 0
  • merge mate pairs 0
  • correction 0
  • reads merging 0
  • short reads 0
  • tab 0
  • immunoprofiling 0
  • trim 0
  • windows 0
  • simulate 0
  • authentication 0
  • allele-specific 0
  • awk 0
  • eido 0
  • blastp 0
  • format 0
  • filtermutectcalls 0
  • samplesheet 0
  • deseq2 0
  • rna-seq 0
  • realignment 0
  • BAM 0
  • validate 0
  • heatmap 0
  • artic 0
  • metagenomic 0
  • eigenstrat 0
  • evidence 0
  • panelofnormals 0
  • regions 0
  • spatial_omics 0
  • random forest 0
  • proteome 0
  • metagenomes 0
  • demultiplexed reads 0
  • aggregate 0
  • edit distance 0
  • RiPP 0
  • baf 0
  • cnv calling 0
  • calling 0
  • scatter 0
  • unaligned 0
  • gwas 0
  • CNV 0
  • norm 0
  • normalize 0
  • repeat_expansions 0
  • UMIs 0
  • eCLIP 0
  • microscopy 0
  • expansionhunterdenovo 0
  • genomad 0
  • intersect 0
  • duplex 0
  • HOPS 0
  • splice 0
  • concat 0
  • tbi 0
  • reheader 0
  • gem 0
  • ChIP-seq 0
  • genome bins 0
  • allele 0
  • estimation 0
  • single cells 0
  • cvnkit 0
  • recombination 0
  • MaltExtract 0
  • vdj 0
  • htseq 0
  • overlapped bed 0
  • bioawk 0
  • unionBedGraphs 0
  • csi 0
  • deduping 0
  • decoy 0
  • multinterval 0
  • boxcox 0
  • tnseq 0
  • bases 0
  • shiftBed 0
  • slopBed 0
  • reverse complement 0
  • plastid 0
  • simulation 0
  • hmmfetch 0
  • clumping fastqs 0
  • propd 0
  • decompose 0
  • sizes 0
  • Read coverage histogram 0
  • region 0
  • transmembrane 0
  • genome graph 0
  • smaller fastqs 0
  • install 0
  • comparative genomics 0
  • sorting 0
  • idx 0
  • rad 0
  • mutect 0
  • autozygosity 0
  • deep variant 0
  • update header 0
  • homozygosity 0
  • biallelic 0
  • structural variant 0
  • file manipulation 0
  • bam2fastx 0
  • bam2fastq 0
  • immcantation 0
  • airrseq 0
  • immunoinformatics 0
  • co-orthology 0
  • homology 0
  • spectral clustering 0
  • sequence similarity 0
  • bamtobed 0
  • gost 0
  • genotypegvcf 0
  • site frequency spectrum 0
  • maskfasta 0
  • joint-genotyping 0
  • sompy 0
  • chunking 0
  • peak picking 0
  • BCF 0
  • introns 0
  • gaps 0
  • transform 0
  • ancestral alleles 0
  • gprofiler2 0
  • derived alleles 0
  • tnfilter 0
  • jaccard 0
  • overlap 0
  • getfasta 0
  • genomecov 0
  • array_cgh 0
  • cytosure 0
  • vector 0
  • genome statistics 0
  • sliding 0
  • clr 0
  • cellpose 0
  • refflat 0
  • gtftogenepred 0
  • ucsc/liftover 0
  • crispr 0
  • antibody capture 0
  • umicollapse 0
  • antigen capture 0
  • scRNA-Seq 0
  • multiomics 0
  • files 0
  • mkvdjref 0
  • upd 0
  • bedtobigbed 0
  • uniparental 0
  • disomy 0
  • snv 0
  • downsample 0
  • downsample bam 0
  • subsample bam 0
  • vcf2db 0
  • gemini 0
  • maf 0
  • lua 0
  • toml 0
  • hifi 0
  • genepred 0
  • bigbed 0
  • uniq 0
  • polymorphic sites 0
  • polymorphic 0
  • detecting svs 0
  • short-read sequencing 0
  • polymut 0
  • svtk/baftest 0
  • baftest 0
  • countsvtypes 0
  • rdtest2vcf 0
  • rdtest 0
  • vcf2bed 0
  • decompress 0
  • bedgraphtobigwig 0
  • chromosome_visualization 0
  • duplicate removal 0
  • chromap 0
  • quality assurnce 0
  • Mycobacterium tuberculosis 0
  • chromosomal rearrangements 0
  • eucaryotes 0
  • coding 0
  • cds 0
  • transcroder 0
  • sequencing adapters 0
  • qa 0
  • vcfbreakmulti 0
  • deduplicate 0
  • alr 0
  • copyratios 0
  • adna 0
  • c to t 0
  • postprocessing 0
  • proteus 0
  • readproteingroups 0
  • tblastn 0
  • eigenvectors 0
  • hicPCA 0
  • snakemake 0
  • workflow 0
  • workflow_mode 0
  • createreadcountpanelofnormals 0
  • denoisereadcounts 0
  • geo 0
  • readwriter 0
  • dnamodelapply 0
  • dnascope 0
  • subtyping 0
  • Salmonella enterica 0
  • sorted 0
  • groupby 0
  • tnscope 0
  • bgen 0
  • chloroplast 0
  • confidence 0
  • blat 0
  • mapad 0
  • yahs 0
  • VCFtools 0
  • calder2 0
  • verifybamid 0
  • DNA contamination estimation 0
  • Assembly 0
  • construct 0
  • graph projection to vcf 0
  • domains 0
  • compartments 0
  • extractunbinned 0
  • linkbins 0
  • topology 0
  • sintax 0
  • vsearch/sort 0
  • usearch 0
  • long read alignment 0
  • pangenome-scale 0
  • all versus all 0
  • mashmap 0
  • wavefront 0
  • whamg 0
  • wham 0
  • cadd 0
  • copy-number 0
  • copy number analysis 0
  • gender determination 0
  • copy number alterations 0
  • raw 0
  • illumiation_correction 0
  • mgf 0
  • bclconvert 0
  • ATACseq 0
  • shift 0
  • ATACshift 0
  • http(s) 0
  • utility 0
  • setgt 0
  • jvarkit 0
  • translate 0
  • tar 0
  • tarball 0
  • targz 0
  • HLA 0
  • nucBed 0
  • vsearch/fastqfilter 0
  • AT content 0
  • nucleotide content 0
  • elfasta 0
  • elprep 0
  • controlstatistics 0
  • source tracking 0
  • emoji 0
  • quality_control 0
  • installation 0
  • doublet_detection 0
  • barcodes 0
  • doCounts 0
  • subsetting 0
  • fastqfilter 0
  • vsearch/dereplicate 0
  • significance statistic 0
  • xml 0
  • ATLAS 0
  • uniques 0
  • Illumina 0
  • functional 0
  • impute-info 0
  • tags 0
  • tag2tag 0
  • sequencing_bias 0
  • hashing-based deconvolution 0
  • rank 0
  • java 0
  • script 0
  • post mortem damage 0
  • svg 0
  • telseq 0
  • standard 0
  • haplotag 0
  • atlas 0
  • staging 0
  • mkarv 0
  • Staging 0
  • microRNA 0
  • multiqc 0
  • mass_error 0
  • search engine 0
  • poolseq 0
  • variant-calling 0
  • stardist 0
  • logFC 0
  • p-value 0
  • Read report 0
  • admixture 0
  • malformed 0
  • fix 0
  • paired reads re-pairing 0
  • regex 0
  • patterns 0
  • doublet 0
  • Immune Deconvolution 0
  • Bioinformatics Tools 0
  • Computational Immunology 0
  • catpack 0
  • prepare 0
  • mzML 0
  • taxonomic composition 0
  • adapterremoval 0
  • chip 0
  • 16S 0
  • hhsuite 0
  • hmmpress 0
  • hmmscan 0
  • phylogenies 0
  • antimicrobial reistance 0
  • junction 0
  • contiguate 0
  • reference panel 0
  • reference compression 0
  • impute 0
  • haploype 0
  • partitioning 0
  • updatedata 0
  • scvi 0
  • AMPs 0
  • solo 0
  • import segmentation 0
  • nuclear segmentation 0
  • cell segmentation 0
  • allele counts 0
  • relabel 0
  • nuclear contamination estimate 0
  • resegment 0
  • morphology 0
  • post Post-processing 0
  • metagenome assembler 0
  • model 0
  • scanpy 0
  • antimicrobial peptide prediction 0
  • run 0
  • plotting 0
  • regtools 0
  • leafcutter 0
  • amp 0
  • recovery 0
  • mgi 0
  • Staphylococcus aureus 0
  • affy 0
  • reference panels 0
  • identity-by-descent 0
  • decomposeblocksub 0
  • block substitutions 0
  • pdb 0
  • drug categorization 0
  • Read trimming 0
  • parquet 0
  • scimap 0
  • cell_phenotyping 0
  • machine_learning 0
  • bamUtil 0
  • bamtools/split 0
  • clahe 0
  • refresh 0
  • association 0
  • GWAS 0
  • case/control 0
  • yaml 0
  • associations 0
  • spatial_neighborhoods 0
  • Bayesian 0
  • n50 0
  • structural-variants 0
  • omics 0
  • biological activity 0
  • bamtools/convert 0
  • prior knowledge 0
  • tag 0
  • cell_barcodes 0
  • mygene 0
  • go 0
  • mouse 0
  • pile up 0
  • bacphlip 0
  • virulent 0
  • cell_type_identification 0
  • seqfu 0
  • lifestyle 0
  • distance-based 0
  • parser 0
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  • standardize 0
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  • quarto 0
  • python 0
  • r 0
  • coexpression 0
  • correlation 0
  • corpcor 0
  • assay 0
  • phylogenetics 0
  • minimum_evolution 0
  • nucleotide sequence 0
  • probabilistic realignment 0
  • homologs 0
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  • multi-tool 0
  • predict 0
  • element 0
  • trimBam 0
  • hardy-weinberg 0
  • hwe statistics 0
  • hwe equilibrium 0
  • reference-independent 0
  • genotype likelihood 0
  • collapse 0
  • liftover 0
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  • nanopore sequencing 0
  • Read filters 0
  • size 0
  • bwamem2 0
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  • grabix 0
  • ribosomal 0
  • 10x 0
  • ancientDNA 0
  • authentict 0
  • regulatory network 0
  • read group 0
  • transcription factors 0
  • paraphase 0
  • selector 0
  • cram-size 0
  • quality check 0
  • Pacbio 0
  • realign 0
  • circular 0
  • spot 0
  • bias 0
  • sage 0
  • mass spectrometry 0
  • featuretable 0
  • extraction 0
  • cgMLST 0
  • WGS 0
  • redundant 0
  • nanoq 0
  • guidetree 0
  • AC/NS/AF 0
  • coreutils 0
  • cobra 0
  • extension 0
  • grea 0
  • autofluorescence 0
  • functional enrichment 0
  • translation 0
  • paired reads merging 0
  • overlap-based merging 0
  • check 0
  • cycif 0
  • hamming-distance 0
  • hashing-based deconvoltion 0
  • gnu 0
  • generic 0
  • vcflib/vcffixup 0
  • transposable element 0
  • background 0
  • single-stranded 0
  • MMseqs2 0
  • InterProScan 0
  • busco 0
  • droplet based single cells 0
  • lexogen 0
  • genotype-based demultiplexing 0
  • donor deconvolution 0
  • cellsnp 0
  • trimfq 0
  • variantcalling 0
  • subcontigs 0
  • streptococcus 0
  • mash/sketch 0
  • maximum-likelihood 0
  • rra 0
  • getpileupsummaries 0
  • cross-samplecontamination 0
  • calculatecontamination 0
  • DNA damage 0
  • NGS 0
  • damage patterns 0
  • estimate 0
  • bedtointervallist 0
  • taxonomic assignment 0
  • asereadcounter 0
  • reduced 0
  • sgRNA 0
  • representations 0
  • vqsr 0
  • maxbin2 0
  • variant quality score recalibration 0
  • metagenome-assembled genomes 0
  • annotateintervals 0
  • mass-spectroscopy 0
  • targets 0
  • mcr-1 0
  • MD5 0
  • 128 bit 0
  • heattree 0
  • megahit 0
  • CRISPR-Cas9 0
  • functional genomics 0
  • debruijn 0
  • short variant discovery 0
  • combining 0
  • determinegermlinecontigploidy 0
  • createsomaticpanelofnormals 0
  • createsequencedictionary 0
  • condensedepthevidence 0
  • dragstr 0
  • composestrtablefile 0
  • adapter removal 0
  • collapsing 0
  • legionella 0
  • peptide prediction 0
  • clinical 0
  • pneumophila 0
  • combinegvcfs 0
  • collectsvevidence 0
  • limma 0
  • Listeria monocytogenes 0
  • collectreadcounts 0
  • cnnscorevariants 0
  • calibratedragstrmodel 0
  • lofreq/call 0
  • lofreq/filter 0
  • qualities 0
  • AMP 0
  • denovo 0
  • gangstr 0
  • kofamscan 0
  • Beautiful stand-alone HTML report 0
  • lint 0
  • random 0
  • generate 0
  • single molecule 0
  • microsatellite instability 0
  • zipperbams 0
  • scan 0
  • mtnucratio 0
  • ratio 0
  • ubam 0
  • mitochondrial to nuclear ratio 0
  • bioinformatics tools 0
  • GATK UnifiedGenotyper 0
  • mosdepth 0
  • SNP table 0
  • contaminant 0
  • unmapped 0
  • sequencing summary 0
  • groupreads 0
  • NextGenMap 0
  • ngm 0
  • Neisseria gonorrhoeae 0
  • gender 0
  • duplexumi 0
  • otu table 0
  • fq 0
  • daa 0
  • metaphlan 0
  • rma6 0
  • Neisseria meningitidis 0
  • k-mer frequency 0
  • gene-calling 0
  • 3D heat map 0
  • contour map 0
  • Merqury 0
  • gamma 0
  • assembly evaluation 0
  • smudgeplot 0
  • ploidy 0
  • unionsum 0
  • UShER 0
  • rust 0
  • methylation bias 0
  • mbias 0
  • bootstrapping 0
  • assembler 0
  • de Bruijn 0
  • bacterial variant calling 0
  • germline variant calling 0
  • somatic variant calling 0
  • variant caller 0
  • duplication metrics 0
  • kegg 0
  • graph construction 0
  • ibd 0
  • gunc 0
  • gunzip 0
  • variantrecalibrator 0
  • recalibration model 0
  • gvcftools 0
  • extract_variants 0
  • extractvariants 0
  • variantfiltration 0
  • abricate 0
  • fARGene 0
  • rgi 0
  • hbd 0
  • archaea 0
  • beagle 0
  • mitochondrial 0
  • svcluster 0
  • svannotate 0
  • splitintervals 0
  • Haemophilus influenzae 0
  • haplotype resolution 0
  • splitcram 0
  • site depth 0
  • shiftintervals 0
  • shiftfasta 0
  • shiftchain 0
  • selectvariants 0
  • gawk 0
  • genome taxonomy database 0
  • gccounter 0
  • genomes on a tree 0
  • gget 0
  • low coverage 0
  • genome summary 0
  • gfastats 0
  • Mykrobe 0
  • Salmonella Typhi 0
  • Sample 0
  • Haplotypes 0
  • Imputation 0
  • joint-variant-calling 0
  • GNU 0
  • merge compare 0
  • repeat content 0
  • txt 0
  • genome heterozygosity 0
  • genome size 0
  • models 0
  • tama_collapse.py 0
  • compound 0
  • genome profile 0
  • gene model 0
  • TAMA 0
  • gstama/merge 0
  • bgc 0
  • file parsing 0
  • gstama/polyacleanup 0
  • GTDB taxonomy 0
  • revert 0
  • reblockgvcf 0
  • estimatelibrarycomplexity 0
  • panelofnormalscreation 0
  • genomic islands 0
  • insertion 0
  • getpileupsumaries 0
  • germlinevariantsites 0
  • germlinecnvcaller 0
  • germline contig ploidy 0
  • jasminesv 0
  • jasmine 0
  • Python 0
  • Jupyter 0
  • jupytext 0
  • papermill 0
  • jointgenotyping 0
  • indexfeaturefile 0
  • genomicsdbimport 0
  • kallisto/index 0
  • quant 0
  • genomicsdb 0
  • gatherbqsrreports 0
  • tranche filtering 0
  • digital normalization 0
  • filtervarianttranches 0
  • k-mer counting 0
  • effective genome size 0
  • filterintervals 0
  • Klebsiella 0
  • pneumoniae 0
  • readcountssummary 0
  • interproscan 0
  • readcounter 0
  • haemophilus 0
  • printsvevidence 0
  • printreads 0
  • preprocessintervals 0
  • HMMER 0
  • amino acid 0
  • postprocessgermlinecnvcalls 0
  • snvs 0
  • Hidden Markov Model 0
  • hmtnote 0
  • annotations 0
  • mutectstats 0
  • pos 0
  • mergebamalignment 0
  • learnreadorientationmodel 0
  • leftalignandtrimvariants 0
  • panel_of_normals 0
  • IDR 0
  • igv 0
  • igv.js 0
  • js 0
  • genome browser 0
  • multicut 0
  • pixel classification 0
  • pixel_classification 0
  • probability_maps 0
  • readorientationartifacts 0
  • population genomics 0
  • consensus sequence 0
  • graph drawing 0
  • gct 0
  • paired-end 0
  • readgroup 0
  • pcr duplicates 0
  • cutesv 0
  • scramble 0
  • cluster analysis 0
  • clusteridentifier 0
  • peak-caller 0
  • cut&tag 0
  • cut&run 0
  • chromatin 0
  • seacr 0
  • assembly-binning 0
  • paired 0
  • cls 0
  • applyvarcal 0
  • VQSR 0
  • variant recalibration 0
  • subseq 0
  • grep 0
  • sertotype 0
  • na 0
  • interleave 0
  • custom 0
  • header 0
  • seq 0
  • read pairs 0
  • repair 0
  • random draw 0
  • rtg-tools 0
  • read_pairs 0
  • fragment_size 0
  • inner_distance 0
  • read distribution 0
  • sequence-based 0
  • mapping-based 0
  • cumulative coverage 0
  • integrity 0
  • rtg 0
  • scatterplot 0
  • pedfilter 0
  • rocplot 0
  • corrrelation 0
  • insert size 0
  • salsa 0
  • salsa2 0
  • LCA 0
  • Ancestor 0
  • multimapper 0
  • flagstat 0
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  • duplicate marking 0
  • amplicon 0
  • ampliconclip 0
  • track 0
  • calmd 0
  • faidx 0
  • selection 0
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  • strandedness 0
  • SNPs 0
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  • core 0
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  • nucleotide composition 0
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  • predictions 0
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  • invariant 0
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  • target 0
  • export 0
  • rRNA 0
  • ribosomal RNA 0
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  • signatures 0
  • hash sketch 0
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  • cmseq 0
  • protein coding genes 0
  • SMN1 0
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  • rare variants 0
  • freqsum 0
  • Cores 0
  • bam2seqz 0
  • gc_wiggle 0
  • induce 0
  • Segmentation 0
  • sex determination 0
  • genetic sex 0
  • relative coverage 0
  • TMA dearray 0
  • UNet 0
  • mcool 0
  • error 0
  • digest 0
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  • antibiotic resistance genes 0
  • motif 0
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  • illumina datasets 0
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  • str 0
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  • CAGE 0
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  • RAMPAGE 0
  • read 0
  • pbp 0
  • STRIPE-seq 0
  • flip 0
  • odgi 0
  • combine graphs 0
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  • graph unchopping 0
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  • HLA-I 0
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A NATA accredited tool for reporting the presence of antimicrobial resistance genes in bacterial genomes

01

matches partials virulence out txt versions

abritamr:

A pipeline for running AMRfinderPlus and collating results into functional classes

Identify antimicrobial resistance in gene or protein sequences

010

report mutation_report versions tool_version db_version

amrfinderplus:

AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences.

Identify antimicrobial resistance in gene or protein sequences

NO input

db versions

amrfinderplus:

AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences.

barrnap uses a hmmer profile to find rrnas in reads or contig fasta files

012

gff versions

For each feature in A, finds the closest feature (upstream or downstream) in B.

0120

output 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.

Retrieve entries from a BLAST database

01201

fasta text versions

blast:

BLAST finds regions of similarity between biological sequences.

Queries a BLAST DNA database

0101

txt versions

blast:

BLAST finds regions of similarity between biological sequences.

Builds a BLAST database

01

db versions

blast:

BLAST finds regions of similarity between biological sequences.

Downloads a BLAST database from NCBI

01

db versions

blast:

BLAST finds regions of similarity between biological sequences.

Find SA coordinates of the input reads for bwa short-read mapping

0101

sai versions

bwa:

BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome.

Perform adapter/quality trimming on sequencing reads

01

reads log versions

cuatadapt:

Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

SV callers like lumpy look at split-reads and pair distances to find structural variants. This tool is a fast way to add depth information to those calls. This can be used as additional information for filtering variants; for example we will be skeptical of deletion calls that do not have lower than average coverage compared to regions with similar gc-content.

01234500

vcf versions

A program that counts sequence occurrences in FASTQ files.

0101

count_matrix stats distribution_plot reads_plot reads_plot_percentage versions

2FAST2Q:

2FAST2Q is ideal for CRISPRi-Seq, and for extracting and counting any kind of information from reads in the fastq format, such as barcodes in Bar-seq experiments. 2FAST2Q can work with sequence mismatches, Phred-score, and be used to find and extract unknown sequences delimited by known sequences. 2FAST2Q can extract multiple features per read using either fixed positions or delimiting search sequences.

A command line tool that makes it easier to find sequencing data from the SRA / GEO / ENA.

0

json versions

A module for concatenation of gzipped or uncompressed files getting around UNIX terminal argument size

01

file_out versions

find:

GNU find searches the directory tree rooted at each given starting-point by evaluating the given expression

pigz:

pigz, which stands for Parallel Implementation of GZip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data.

A module for decompressing a large number of gzipped files, getting around the UNIX terminal argument limit

01

file_out versions

find:

GNU find searches the directory tree rooted at each given starting-point by evaluating the given expression

pigz:

pigz, which stands for Parallel Implementation of GZip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data.

Tool to convert and summarize AMRfinderPlus outputs using the hAMRonization specification.

01000

json tsv versions

hamronization:

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

Find peaks with HOMER suite

010

txt versions

homer:

HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.

Makes a dotplot (Oxford Grid) of pair-wise sequence alignments

0120100

gif png versions

last:

LAST finds & aligns related regions of sequences.

Aligns query sequences to target sequences indexed with lastdb

0120

maf multiqc versions

last:

LAST finds & aligns related regions of sequences.

Prepare sequences for subsequent alignment with lastal.

01

index versions

last:

LAST finds & aligns related regions of sequences.

Converts MAF alignments in another format.

012010101

axt_gz bam blast_gz blasttab_gz chain_gz cram gff_gz html_gz psl_gz sam_gz tab_gz versions

last:

LAST finds & aligns related regions of sequences.

Reorder alignments in a MAF file

01

maf versions

last:

LAST finds & aligns related regions of sequences.

Post-alignment masking

01

maf versions

last:

LAST finds & aligns related regions of sequences.

Find split or spliced alignments in a MAF file

01

maf multiqc versions

last:

LAST finds & aligns related regions of sequences.

Find suitable score parameters for sequence alignment

010

param_file multiqc versions

last:

LAST finds & aligns related regions of sequences.

Finds full-length LTR retrotranspsons in genome sequences using the parallel version of LTR_Finder

01

scn gff versions

LTR_FINDER_parallel:

A Perl wrapper for LTR_FINDER

LTR_Finder:

An efficient program for finding full-length LTR retrotranspsons in genome sequences

Identifies LTR retrotransposons using LTR_retriever

metagenomeharvestfindermgescannon_tgca

meta log pass_list pass_list_gff ltrlib annotation_out annotation_gff versions

LTR_retriever:

Sensitive and accurate identification of LTR retrotransposons

marks duplicate spots along gridline edges.

01

marked_dups_spots versions

mindagap:

Takes a single panorama image and fills the empty grid lines with neighbour-weighted values.

miRanda is an algorithm for finding genomic targets for microRNAs

010

txt versions

Download a mitochondrial genome to be used as reference for MitoHiFi

01

fasta gb versions

findMitoReference.py:

Fetch mitochondrial genome in Fasta and Genbank format from NCBI

Parse all the supporting reads of putative somatic SVs using nanomonsv. After successful completion, you will find supporting reads stratified by deletions, insertions, and rearrangements. A precursor to "nanomonsv get"

012

insertions insertions_index deletions deletions_index rearrangements rearrangements_index bp_info bp_info_index versions

nanomonsv:

nanomonsv is a software for detecting somatic structural variations from paired (tumor and matched control) cancer genome sequence data.

OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics.

0101

orthofinder working versions

Find and remove PCR/optical duplicates

01

pairs stat versions

pairtools:

CLI tools to process mapped Hi-C data

Find ligation junctions in .sam, make .pairs

010

pairsam stat versions

pairtools:

CLI tools to process mapped Hi-C data

Paraclu finds clusters in data attached to sequences.

010

bed versions

Predict prophages in bacterial genomes

01

coordinates gbk log information bacteria_fasta bacteria_gbk phage_fasta phage_gbk prophage_gff prophage_tbl prophage_tsv versions

phispy:

Prophage finder using multiple metrics

Automatically improve draft assemblies and find variation among strains, including large event detection

010120

improved_assembly vcf change_record tracks_bed tracks_wig versions

Identify plasmids in bacterial sequences and assemblies

01

json txt tsv genome_seq plasmid_seq versions

Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program

010

gene_annotations nucleotide_fasta amino_acid_fasta all_gene_annotations versions

ResFinder identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria

01200

json disinfinder_kma pheno_table_species pheno_table pointfinder_kma pointfinder_prediction pointfinder_results pointfinder_table resfinder_hit_in_genome_seq resfinder_blast resfinder_kma resfinder_resistance_gene_seq resfinder_results_table resfinder_results_tab resfinder_results versions

resfinder:

ResFinder identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria

find and mark duplicate reads in BAM file

01

bam bai versions

sambamba:

process your BAM data faster!

Use seqkit to find/replace strings within sequences and sequence headers

01

fastx versions

seqkit:

Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.

Determine Shigella serotype from assemblies or Illumina paired-end reads

01

tsv versions

Computational method for finding spa types.

0100

tsv versions

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

01

results_xlsx summary_tsv detailed_summary_tsv resfinder_tsv plasmidfinder_tsv mlst_tsv settings_txt pointfinder_tsv versions

staramr:

Scan genome contigs against the ResFinder and PointFinder databases. In order to use the PointFinder databases, you will have to add --pointfinder-organism ORGANISM to the ext.args options.

Serotype STEC samples from paired-end reads or assemblies

01

tsv versions

Sylph profile command for taxonoming profiling

010

profile_out versions

sylph:

Sylph quickly enables querying of genomes against even low-coverage shotgun metagenomes to find nearest neighbour ANI.

Sketching/indexing sequencing reads

010

sketch_fastq_genome versions

sylph:

Sylph quickly enables querying of genomes against even low-coverage shotgun metagenomes to find nearest neighbour ANI.

Estimating poly(A)-tail lengths from basecalled fast5 files produced by Nanopore sequencing of RNA and DNA

01

csv_gz versions

tidk explore attempts to find the simple telomeric repeat unit in the genome provided. It will report this repeat in its canonical form (e.g. TTAGG -> AACCT).

01

explore_tsv top_sequence versions

tidk:

tidk is a toolkit to identify and visualise telomeric repeats in genomes

Velocyto is a library for the analysis of RNA velocity. velocyto.py CLI use Path(resolve_path=True) and breaks the nextflow logic of symbolic links. If in the work dir velocyto find a file named EXACTLY cellsorted_[ORIGINAL_BAM_NAME] it will skip the samtools sort step. Cellsorted bam file should be cell sorted with:

    samtools sort -t CB -O BAM -o cellsorted_input.bam input.bam

See module test for an example with the SAMTOOLS_SORT nf-core module. Config example to cellsort input bam using SAMTOOLS_SORT:

    withName: SAMTOOLS_SORT {
        ext.prefix = { "cellsorted_${bam.baseName}" }
        ext.args = '-t CB -O BAM'
    }

Optional mask must be passed with ext.args and option --mask This is why I need to stage in the work dir 2 bam files (cellsorted and original). See also velocyto tutorial

01230

loom versions

Find copy number aberrations

010101

aberrations_bed bins_bed segments_bed chr_statistics chr_plots genome_plot versions

wisecondorx:

WIthin-SamplE COpy Number aberration DetectOR, including sex chromosomes

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