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.

  • bam 3
  • fasta 3
  • vcf 3
  • genomics 2
  • sequence 2
  • reheader 2
  • fastq 1
  • cram 1
  • sort 1
  • annotation 1
  • align 1
  • filter 1
  • gff 1
  • bcftools 1
  • protein 1
  • picard 1
  • bcf 1
  • gff3 1
  • seqkit 1
  • fastx 1
  • replace 1
  • dictionary 1
  • clean 1
  • ped 1
  • reformatting 1
  • rtgtools 1
  • dereplicate 1
  • rename 1
  • functional 1
  • uniques 1
  • pdb 1
  • sequence headers 1
  • header 1
  • pedfilter 1
  • duplicate marking 1
  • update header 1
  • metagenomics 0
  • genome 0
  • index 0
  • reference 0
  • alignment 0
  • assembly 0
  • bed 0
  • gatk4 0
  • sam 0
  • structural variants 0
  • variant calling 0
  • database 0
  • merge 0
  • bacteria 0
  • map 0
  • statistics 0
  • coverage 0
  • qc 0
  • variants 0
  • quality control 0
  • classification 0
  • download 0
  • classify 0
  • gtf 0
  • nanopore 0
  • cnv 0
  • split 0
  • gfa 0
  • taxonomic profiling 0
  • k-mer 0
  • variant 0
  • MSA 0
  • contamination 0
  • somatic 0
  • pacbio 0
  • taxonomy 0
  • sentieon 0
  • convert 0
  • count 0
  • proteomics 0
  • binning 0
  • quality 0
  • conversion 0
  • single-cell 0
  • VCF 0
  • copy number 0
  • clustering 0
  • ancient DNA 0
  • bedtools 0
  • imputation 0
  • phylogeny 0
  • contigs 0
  • bisulfite 0
  • mags 0
  • reporting 0
  • graph 0
  • variation graph 0
  • sv 0
  • isoseq 0
  • build 0
  • trimming 0
  • long reads 0
  • gvcf 0
  • kmer 0
  • cna 0
  • rnaseq 0
  • wgs 0
  • illumina 0
  • bqsr 0
  • databases 0
  • QC 0
  • compression 0
  • indexing 0
  • bisulphite 0
  • methylseq 0
  • consensus 0
  • methylation 0
  • table 0
  • metrics 0
  • imaging 0
  • antimicrobial resistance 0
  • taxonomic classification 0
  • long-read 0
  • phage 0
  • 5mC 0
  • mapping 0
  • visualisation 0
  • stats 0
  • demultiplex 0
  • openms 0
  • tsv 0
  • sequences 0
  • serotype 0
  • protein sequence 0
  • amr 0
  • base quality score recalibration 0
  • haplotype 0
  • histogram 0
  • scWGBS 0
  • WGBS 0
  • pairs 0
  • DNA methylation 0
  • pangenome graph 0
  • markduplicates 0
  • bins 0
  • searching 0
  • depth 0
  • cluster 0
  • aDNA 0
  • structure 0
  • plot 0
  • neural network 0
  • matrix 0
  • expression 0
  • validation 0
  • checkm 0
  • LAST 0
  • metagenome 0
  • genotype 0
  • completeness 0
  • archaeogenomics 0
  • repeat 0
  • biscuit 0
  • mmseqs2 0
  • palaeogenomics 0
  • virus 0
  • damage 0
  • mappability 0
  • filtering 0
  • annotate 0
  • db 0
  • bisulfite sequencing 0
  • cooler 0
  • bwa 0
  • aligner 0
  • low-coverage 0
  • samtools 0
  • iCLIP 0
  • machine learning 0
  • transcript 0
  • msa 0
  • hmmsearch 0
  • segmentation 0
  • decompression 0
  • mkref 0
  • dedup 0
  • peaks 0
  • population genetics 0
  • phasing 0
  • mag 0
  • transcriptome 0
  • kraken2 0
  • glimpse 0
  • bismark 0
  • blast 0
  • example 0
  • evaluation 0
  • genotyping 0
  • umi 0
  • ncbi 0
  • spatial 0
  • germline 0
  • ucsc 0
  • newick 0
  • gene 0
  • complexity 0
  • feature 0
  • json 0
  • demultiplexing 0
  • prediction 0
  • mirna 0
  • antimicrobial resistance genes 0
  • report 0
  • bedGraph 0
  • deduplication 0
  • vsearch 0
  • antimicrobial peptides 0
  • differential 0
  • prokaryote 0
  • low frequency variant calling 0
  • cnvkit 0
  • scRNA-seq 0
  • kmers 0
  • tumor-only 0
  • pangenome 0
  • mitochondria 0
  • splicing 0
  • gzip 0
  • plasmid 0
  • hmmer 0
  • snp 0
  • single 0
  • duplicates 0
  • NCBI 0
  • short-read 0
  • multiple sequence alignment 0
  • amps 0
  • visualization 0
  • de novo 0
  • merging 0
  • benchmark 0
  • adapters 0
  • kallisto 0
  • summary 0
  • fragment 0
  • single cell 0
  • svtk 0
  • mem 0
  • arg 0
  • 3-letter genome 0
  • ptr 0
  • call 0
  • gridss 0
  • coptr 0
  • detection 0
  • query 0
  • profiling 0
  • diversity 0
  • mutect2 0
  • idXML 0
  • view 0
  • antibiotic resistance 0
  • interval 0
  • indels 0
  • mpileup 0
  • counts 0
  • tabular 0
  • microbiome 0
  • extract 0
  • csv 0
  • sourmash 0
  • deamination 0
  • riboseq 0
  • MAF 0
  • isolates 0
  • de novo assembly 0
  • text 0
  • wxs 0
  • clipping 0
  • cut 0
  • genome assembler 0
  • CLIP 0
  • bedgraph 0
  • bcl2fastq 0
  • archaeogenetics 0
  • bin 0
  • SV 0
  • haplotypecaller 0
  • circrna 0
  • STR 0
  • structural 0
  • gsea 0
  • interval_list 0
  • genmod 0
  • hic 0
  • miscoding lesions 0
  • diamond 0
  • public datasets 0
  • fgbio 0
  • bigwig 0
  • compress 0
  • compare 0
  • peak-calling 0
  • profile 0
  • snps 0
  • palaeogenetics 0
  • enrichment 0
  • phylogenetic placement 0
  • ranking 0
  • ganon 0
  • read depth 0
  • deep learning 0
  • paf 0
  • cat 0
  • ngscheckmate 0
  • matching 0
  • malt 0
  • telomere 0
  • concatenate 0
  • redundancy 0
  • union 0
  • ATAC-seq 0
  • family 0
  • bgzip 0
  • add 0
  • sketch 0
  • retrotransposon 0
  • BGC 0
  • normalization 0
  • biosynthetic gene cluster 0
  • fungi 0
  • propr 0
  • logratio 0
  • copy number alteration calling 0
  • hybrid capture sequencing 0
  • targeted sequencing 0
  • DNA sequencing 0
  • chunk 0
  • sequencing 0
  • reads 0
  • microsatellite 0
  • FASTQ 0
  • microarray 0
  • happy 0
  • ont 0
  • umitools 0
  • HiFi 0
  • hmmcopy 0
  • xeniumranger 0
  • ancestry 0
  • ccs 0
  • abundance 0
  • pypgx 0
  • isomir 0
  • reference-free 0
  • DNA sequence 0
  • sample 0
  • containment 0
  • ampir 0
  • parsing 0
  • preprocessing 0
  • resistance 0
  • quantification 0
  • mapper 0
  • amplicon sequences 0
  • typing 0
  • windowmasker 0
  • uncompress 0
  • untar 0
  • unzip 0
  • vrhyme 0
  • entrez 0
  • fastk 0
  • zip 0
  • npz 0
  • bedpe 0
  • guide tree 0
  • RNA 0
  • repeat expansion 0
  • fcs-gx 0
  • fingerprint 0
  • PCA 0
  • miRNA 0
  • ambient RNA removal 0
  • transcriptomics 0
  • rna_structure 0
  • genotype-based deconvoltion 0
  • variant_calling 0
  • popscle 0
  • transposons 0
  • bacterial 0
  • organelle 0
  • gatk4spark 0
  • mzml 0
  • somatic variants 0
  • mtDNA 0
  • long_read 0
  • subsample 0
  • minimap2 0
  • html 0
  • covid 0
  • pan-genome 0
  • pairsam 0
  • score 0
  • mlst 0
  • genome assembly 0
  • polishing 0
  • transcripts 0
  • small indels 0
  • panel 0
  • krona 0
  • lineage 0
  • pseudoalignment 0
  • krona chart 0
  • reports 0
  • ligate 0
  • notebook 0
  • amplicon sequencing 0
  • dna 0
  • cfDNA 0
  • HMM 0
  • chimeras 0
  • PacBio 0
  • pangolin 0
  • structural_variants 0
  • uLTRA 0
  • SNP 0
  • tabix 0
  • survivor 0
  • UMI 0
  • spaceranger 0
  • informative sites 0
  • kinship 0
  • identity 0
  • relatedness 0
  • lossless 0
  • observations 0
  • shapeit 0
  • benchmarking 0
  • duplication 0
  • rsem 0
  • wastewater 0
  • indel 0
  • spark 0
  • prokka 0
  • plink2 0
  • fam 0
  • bim 0
  • insert 0
  • scores 0
  • archiving 0
  • converter 0
  • roh 0
  • dump 0
  • prefetch 0
  • kraken 0
  • arriba 0
  • fusion 0
  • cut up 0
  • mcmicro 0
  • pileup 0
  • image_analysis 0
  • quality trimming 0
  • hi-c 0
  • CRISPR 0
  • gene expression 0
  • eukaryotes 0
  • remove 0
  • cellranger 0
  • cool 0
  • virulence 0
  • bakta 0
  • combine 0
  • mkfastq 0
  • bamtools 0
  • nucleotide 0
  • chromosome 0
  • prokaryotes 0
  • DRAMP 0
  • comparisons 0
  • image 0
  • fai 0
  • microbes 0
  • neubi 0
  • chip-seq 0
  • host 0
  • png 0
  • C to T 0
  • das tool 0
  • das_tool 0
  • bwameth 0
  • deeparg 0
  • complement 0
  • ataqv 0
  • wig 0
  • amplify 0
  • macrel 0
  • highly_multiplexed_imaging 0
  • genomes 0
  • aln 0
  • RNA-seq 0
  • atac-seq 0
  • rna 0
  • angsd 0
  • bracken 0
  • adapter trimming 0
  • genome mining 0
  • intervals 0
  • checkv 0
  • genetics 0
  • metamaps 0
  • concat 0
  • mask 0
  • ichorcna 0
  • hlala_typing 0
  • hla_typing 0
  • vcflib 0
  • functional analysis 0
  • hidden Markov model 0
  • hlala 0
  • lift 0
  • vg 0
  • leviosam2 0
  • hla 0
  • mapcounter 0
  • read-group 0
  • gene set analysis 0
  • interactions 0
  • aggregate 0
  • RNA-Seq 0
  • genome bins 0
  • simulate 0
  • ChIP-seq 0
  • import 0
  • artic 0
  • adapter 0
  • single cells 0
  • demultiplexed reads 0
  • genomad 0
  • preseq 0
  • library 0
  • gem 0
  • allele 0
  • amptransformer 0
  • ampgram 0
  • regression 0
  • differential expression 0
  • taxids 0
  • taxon name 0
  • zlib 0
  • trancriptome 0
  • tama 0
  • gstama 0
  • immunoprofiling 0
  • concordance 0
  • gene set 0
  • vdj 0
  • variation 0
  • phase 0
  • bfiles 0
  • variant pruning 0
  • tbi 0
  • norm 0
  • orf 0
  • tree 0
  • megan 0
  • orthology 0
  • parallelized 0
  • windows 0
  • checksum 0
  • removal 0
  • transcriptomic 0
  • mudskipper 0
  • mitochondrion 0
  • intersection 0
  • edit distance 0
  • minhash 0
  • authentication 0
  • mash 0
  • nextclade 0
  • distance 0
  • registration 0
  • image_processing 0
  • NRPS 0
  • GC content 0
  • xz 0
  • resolve_bioscience 0
  • multiallelic 0
  • small variants 0
  • nucleotides 0
  • rgfa 0
  • cnvnator 0
  • homoploymer 0
  • tnhaplotyper2 0
  • spatial_transcriptomics 0
  • comparison 0
  • proportionality 0
  • secondary metabolites 0
  • profiles 0
  • MSI 0
  • instability 0
  • msi 0
  • tumor 0
  • micro-satellite-scan 0
  • msisensor-pro 0
  • RiPP 0
  • archive 0
  • instrain 0
  • trim 0
  • khmer 0
  • bustools 0
  • awk 0
  • salmon 0
  • BAM 0
  • blastn 0
  • scatter 0
  • normalize 0
  • screen 0
  • antismash 0
  • GPU-accelerated 0
  • polyA_tail 0
  • refine 0
  • maximum likelihood 0
  • iphop 0
  • intersect 0
  • proteome 0
  • ancient dna 0
  • kma 0
  • graph layout 0
  • primer 0
  • COBS 0
  • k-mer index 0
  • bloom filter 0
  • HOPS 0
  • lofreq 0
  • serogroup 0
  • antibiotics 0
  • barcode 0
  • pharokka 0
  • SimpleAF 0
  • function 0
  • MaltExtract 0
  • retrotransposons 0
  • long terminal repeat 0
  • pair 0
  • interactive 0
  • krakenuniq 0
  • long terminal retrotransposon 0
  • krakentools 0
  • baf 0
  • duplex 0
  • cvnkit 0
  • cleaning 0
  • sequence analysis 0
  • correction 0
  • long-read sequencing 0
  • frame-shift correction 0
  • signature 0
  • microbial 0
  • tab 0
  • trgt 0
  • scaffolding 0
  • varcal 0
  • realignment 0
  • Pharmacogenetics 0
  • gwas 0
  • graft 0
  • deconvolution 0
  • small genome 0
  • estimation 0
  • de novo assembler 0
  • corrupted 0
  • emboss 0
  • nacho 0
  • interval list 0
  • nanostring 0
  • mRNA 0
  • salmonella 0
  • settings 0
  • filtermutectcalls 0
  • junctions 0
  • metadata 0
  • bayesian 0
  • seqtk 0
  • short reads 0
  • UMIs 0
  • xenograft 0
  • unaligned 0
  • fetch 0
  • join 0
  • GEO 0
  • soft-clipped clusters 0
  • cancer genomics 0
  • anndata 0
  • snpsift 0
  • gene labels 0
  • fixmate 0
  • metagenomic 0
  • doublets 0
  • reads merging 0
  • screening 0
  • pharmacogenetics 0
  • FracMinHash sketch 0
  • fusions 0
  • repeat_expansions 0
  • expansionhunterdenovo 0
  • CNV 0
  • cnv calling 0
  • effect prediction 0
  • merge mate pairs 0
  • snpeff 0
  • bam2fq 0
  • calling 0
  • collate 0
  • dict 0
  • identifier 0
  • sra-tools 0
  • allele-specific 0
  • smrnaseq 0
  • Duplication purging 0
  • taxon tables 0
  • fasterq-dump 0
  • sequenzautils 0
  • otu tables 0
  • recombination 0
  • standardisation 0
  • eCLIP 0
  • repeats 0
  • standardise 0
  • runs_of_homozygosity 0
  • transformation 0
  • ome-tif 0
  • standardization 0
  • taxonomic profile 0
  • polish 0
  • Read depth 0
  • shigella 0
  • joint genotyping 0
  • gatk 0
  • scaffold 0
  • contig 0
  • duplicate 0
  • regions 0
  • blastp 0
  • eido 0
  • MCMICRO 0
  • eigenstrat 0
  • spatial_omics 0
  • heatmap 0
  • Streptococcus pneumoniae 0
  • random forest 0
  • RNA sequencing 0
  • mirdeep2 0
  • evidence 0
  • metagenomes 0
  • structural-variant calling 0
  • svdb 0
  • parse 0
  • samplesheet 0
  • deseq2 0
  • switch 0
  • validate 0
  • panelofnormals 0
  • purge duplications 0
  • format 0
  • rna-seq 0
  • workflow 0
  • longread 0
  • dist 0
  • snakemake 0
  • rare variants 0
  • reverse complement 0
  • eigenvectors 0
  • hicPCA 0
  • de-novo 0
  • error 0
  • dbnsfp 0
  • sliding 0
  • POA 0
  • snippy 0
  • predictions 0
  • CRAM 0
  • autofluorescence 0
  • groupby 0
  • sliding window 0
  • tnscope 0
  • bgen 0
  • boxplot 0
  • dnascope 0
  • clr 0
  • alr 0
  • features 0
  • density 0
  • blat 0
  • chloroplast 0
  • SMN1 0
  • dnamodelapply 0
  • Read coverage histogram 0
  • confidence 0
  • core 0
  • workflow_mode 0
  • sha256 0
  • sniffles 0
  • createreadcountpanelofnormals 0
  • 256 bit 0
  • SMN2 0
  • boxcox 0
  • copyratios 0
  • propd 0
  • shinyngs 0
  • denoisereadcounts 0
  • readwriter 0
  • Escherichia coli 0
  • exploratory 0
  • cds 0
  • copy-number 0
  • readproteingroups 0
  • subsample bam 0
  • estimate 0
  • svtk/baftest 0
  • upd 0
  • uniparental 0
  • disomy 0
  • snv 0
  • sequencing_bias 0
  • downsample 0
  • downsample bam 0
  • short-read sequencing 0
  • countsvtypes 0
  • vcf2db 0
  • detecting svs 0
  • gemini 0
  • maf 0
  • lua 0
  • ATLAS 0
  • bias 0
  • variantcalling 0
  • sccmec 0
  • streptococcus 0
  • baftest 0
  • rdtest2vcf 0
  • spa 0
  • refflat 0
  • transcroder 0
  • sequencing adapters 0
  • atlas 0
  • bedgraphtobigwig 0
  • bigbed 0
  • bedtobigbed 0
  • eucaryotes 0
  • genepred 0
  • chromosomal rearrangements 0
  • gtftogenepred 0
  • rdtest 0
  • Mycobacterium tuberculosis 0
  • ucsc/liftover 0
  • mkarv 0
  • fast5 0
  • umicollapse 0
  • polya tail 0
  • post mortem damage 0
  • decompress 0
  • files 0
  • vcf2bed 0
  • toml 0
  • spatype 0
  • proteus 0
  • background 0
  • whamg 0
  • rRNA 0
  • wham 0
  • HLA 0
  • coding 0
  • ancientDNA 0
  • single-stranded 0
  • copy number analysis 0
  • gender determination 0
  • cycif 0
  • mashmap 0
  • copy number alterations 0
  • constant 0
  • copy number variation 0
  • yahs 0
  • geo 0
  • mapad 0
  • invariant 0
  • SNPs 0
  • adna 0
  • c to t 0
  • wavefront 0
  • all versus all 0
  • vcfbreakmulti 0
  • read group 0
  • uniq 0
  • deduplicate 0
  • VCFtools 0
  • verifybamid 0
  • DNA contamination estimation 0
  • construct 0
  • graph projection to vcf 0
  • http(s) 0
  • extractunbinned 0
  • fracminhash sketch 0
  • ribosomal RNA 0
  • hash sketch 0
  • linkbins 0
  • signatures 0
  • utility 0
  • sintax 0
  • vsearch/sort 0
  • authentict 0
  • usearch 0
  • long read alignment 0
  • pangenome-scale 0
  • scRNA-Seq 0
  • mgf 0
  • simulation 0
  • affy 0
  • tags 0
  • tag2tag 0
  • Staphylococcus aureus 0
  • hashing-based deconvolution 0
  • rank 0
  • java 0
  • script 0
  • xml 0
  • svg 0
  • standard 0
  • haplotag 0
  • staging 0
  • Staging 0
  • microRNA 0
  • multiqc 0
  • mass_error 0
  • search engine 0
  • poolseq 0
  • variant-calling 0
  • stardist 0
  • telseq 0
  • vsearch/dereplicate 0
  • vsearch/fastqfilter 0
  • fastqfilter 0
  • ATACseq 0
  • shift 0
  • ATACshift 0
  • setgt 0
  • impute-info 0
  • Illumina 0
  • translate 0
  • circular 0
  • bwamem2 0
  • bwameme 0
  • grabix 0
  • ribosomal 0
  • 10x 0
  • regulatory network 0
  • transcription factors 0
  • paraphase 0
  • selector 0
  • cram-size 0
  • size 0
  • quality check 0
  • realign 0
  • spot 0
  • orthogroup 0
  • orthologs 0
  • sage 0
  • mass spectrometry 0
  • featuretable 0
  • extraction 0
  • cgMLST 0
  • WGS 0
  • redundant 0
  • nanoq 0
  • Read filters 0
  • Read trimming 0
  • Read report 0
  • drug categorization 0
  • jvarkit 0
  • tar 0
  • Pacbio 0
  • run 0
  • scanpy 0
  • contiguate 0
  • plotting 0
  • regtools 0
  • leafcutter 0
  • split_kmers 0
  • recovery 0
  • mgi 0
  • sylph 0
  • identity-by-descent 0
  • decomposeblocksub 0
  • block substitutions 0
  • updatedata 0
  • human removal 0
  • chip 0
  • partitioning 0
  • malformed 0
  • fix 0
  • paired reads re-pairing 0
  • regex 0
  • patterns 0
  • doublet 0
  • Immune Deconvolution 0
  • Bioinformatics Tools 0
  • Computational Immunology 0
  • catpack 0
  • prepare 0
  • mzML 0
  • metagenome assembler 0
  • decontamination 0
  • tarball 0
  • doublet_detection 0
  • targz 0
  • bclconvert 0
  • nucBed 0
  • AT content 0
  • nucleotide content 0
  • elfasta 0
  • elprep 0
  • controlstatistics 0
  • source tracking 0
  • emoji 0
  • quality_control 0
  • reference panels 0
  • admixture 0
  • barcodes 0
  • hostile 0
  • subsetting 0
  • logFC 0
  • significance statistic 0
  • p-value 0
  • scvi 0
  • solo 0
  • import segmentation 0
  • nuclear segmentation 0
  • cell segmentation 0
  • adapterremoval 0
  • relabel 0
  • resegment 0
  • morphology 0
  • antimicrobial reistance 0
  • guidetree 0
  • AC/NS/AF 0
  • hmmfetch 0
  • AMPs 0
  • sequence similarity 0
  • spectral clustering 0
  • comparative genomics 0
  • deep variant 0
  • mutect 0
  • idx 0
  • transform 0
  • gaps 0
  • introns 0
  • install 0
  • joint-genotyping 0
  • genotypegvcf 0
  • model 0
  • parallel 0
  • co-orthology 0
  • plastid 0
  • resfinder 0
  • resistance genes 0
  • raw 0
  • parquet 0
  • parser 0
  • dbsnp 0
  • standardize 0
  • quarto 0
  • python 0
  • r 0
  • coexpression 0
  • correlation 0
  • corpcor 0
  • homology 0
  • immunoinformatics 0
  • phylogenetics 0
  • site frequency spectrum 0
  • decompose 0
  • transmembrane 0
  • genome graph 0
  • tnseq 0
  • decoy 0
  • htseq 0
  • rrna 0
  • installation 0
  • sompy 0
  • doCounts 0
  • purging 0
  • peak picking 0
  • allele counts 0
  • ancestral alleles 0
  • airrseq 0
  • derived alleles 0
  • tnfilter 0
  • nuclear contamination estimate 0
  • array_cgh 0
  • cytosure 0
  • post Post-processing 0
  • vector 0
  • gprofiler2 0
  • gost 0
  • rad 0
  • structural variant 0
  • bam2fastx 0
  • bam2fastq 0
  • immcantation 0
  • assay 0
  • minimum_evolution 0
  • vcflib/vcffixup 0
  • hamming-distance 0
  • mygene 0
  • go 0
  • pile up 0
  • nanopore sequencing 0
  • rna velocity 0
  • cobra 0
  • extension 0
  • grea 0
  • functional enrichment 0
  • translation 0
  • paired reads merging 0
  • overlap-based merging 0
  • check 0
  • hashing-based deconvoltion 0
  • tag 0
  • gnu 0
  • coreutils 0
  • generic 0
  • transposable element 0
  • retrieval 0
  • MMseqs2 0
  • InterProScan 0
  • busco 0
  • droplet based single cells 0
  • lexogen 0
  • genotype-based demultiplexing 0
  • donor deconvolution 0
  • cellsnp 0
  • trimfq 0
  • cell_barcodes 0
  • prior knowledge 0
  • distance-based 0
  • seqfu 0
  • nucleotide sequence 0
  • homologs 0
  • antimicrobial peptide prediction 0
  • multi-tool 0
  • predict 0
  • amp 0
  • hardy-weinberg 0
  • hwe statistics 0
  • hwe equilibrium 0
  • reference-independent 0
  • genotype likelihood 0
  • collapse 0
  • liftover 0
  • probabilistic realignment 0
  • n50 0
  • biological activity 0
  • cell_type_identification 0
  • cell_phenotyping 0
  • machine_learning 0
  • clahe 0
  • refresh 0
  • association 0
  • GWAS 0
  • case/control 0
  • associations 0
  • spatial_neighborhoods 0
  • scimap 0
  • Bayesian 0
  • structural-variants 0
  • omics 0
  • lifestyle 0
  • cadd 0
  • relative coverage 0
  • genomes on a tree 0
  • genome manipulation 0
  • genome statistics 0
  • gget 0
  • low coverage 0
  • crispr 0
  • antibody capture 0
  • antigen capture 0
  • Sample 0
  • Haplotypes 0
  • Imputation 0
  • joint-variant-calling 0
  • GNU 0
  • merge compare 0
  • multiomics 0
  • gfastats 0
  • tama_collapse.py 0
  • gene model 0
  • TAMA 0
  • gstama/merge 0
  • gstama/polyacleanup 0
  • GTDB taxonomy 0
  • mkvdjref 0
  • genome taxonomy database 0
  • archaea 0
  • gunc 0
  • gunzip 0
  • cellpose 0
  • gvcftools 0
  • extract_variants 0
  • genome summary 0
  • qa 0
  • abricate 0
  • variantrecalibrator 0
  • reblockgvcf 0
  • revert 0
  • selectvariants 0
  • shiftchain 0
  • shiftfasta 0
  • shiftintervals 0
  • site depth 0
  • splitcram 0
  • splitintervals 0
  • svannotate 0
  • svcluster 0
  • variantfiltration 0
  • recalibration model 0
  • gawk 0
  • quality assurnce 0
  • txt 0
  • file parsing 0
  • bgc 0
  • chromosome_visualization 0
  • genome profile 0
  • duplicate removal 0
  • compound 0
  • models 0
  • chromap 0
  • genome size 0
  • genome heterozygosity 0
  • repeat content 0
  • Salmonella Typhi 0
  • Mykrobe 0
  • extractvariants 0
  • amrfinderplus 0
  • printreads 0
  • subtyping 0
  • probability_maps 0
  • population genomics 0
  • interproscan 0
  • genomic islands 0
  • insertion 0
  • postprocessing 0
  • jasminesv 0
  • jasmine 0
  • Python 0
  • Jupyter 0
  • jupytext 0
  • papermill 0
  • tblastn 0
  • Salmonella enterica 0
  • pixel classification 0
  • kallisto/index 0
  • quant 0
  • sorted 0
  • digital normalization 0
  • k-mer counting 0
  • effective genome size 0
  • Klebsiella 0
  • pneumoniae 0
  • file manipulation 0
  • kegg 0
  • kofamscan 0
  • combining 0
  • bioawk 0
  • unionBedGraphs 0
  • pixel_classification 0
  • multicut 0
  • fARGene 0
  • readcounter 0
  • rgi 0
  • ibd 0
  • hbd 0
  • beagle 0
  • mitochondrial 0
  • haplogroups 0
  • hifi 0
  • Assembly 0
  • Haemophilus influenzae 0
  • haplotype resolution 0
  • domains 0
  • compartments 0
  • topology 0
  • gccounter 0
  • calder2 0
  • genome browser 0
  • reformat 0
  • HMMER 0
  • amino acid 0
  • track 0
  • Hidden Markov Model 0
  • hmtnote 0
  • annotations 0
  • pos 0
  • haemophilus 0
  • panel_of_normals 0
  • IDR 0
  • igv 0
  • igv.js 0
  • js 0
  • printsvevidence 0
  • preprocessintervals 0
  • reorder 0
  • ENA 0
  • TMA dearray 0
  • UNet 0
  • mcool 0
  • genomic bins 0
  • makebins 0
  • str 0
  • faqcs 0
  • antibiotic resistance genes 0
  • ARGs 0
  • ANI 0
  • enzyme 0
  • digest 0
  • SRA 0
  • public 0
  • Cores 0
  • cload 0
  • cooler/balance 0
  • consensus sequence 0
  • duplexumi 0
  • groupreads 0
  • unmapped 0
  • ubam 0
  • zipperbams 0
  • subcontigs 0
  • nucleotide composition 0
  • concoct 0
  • single molecule 0
  • generate 0
  • random 0
  • Segmentation 0
  • cache 0
  • fq 0
  • PEP 0
  • corrrelation 0
  • scatterplot 0
  • cumulative coverage 0
  • paired-end 0
  • pcr duplicates 0
  • blastx 0
  • cutesv 0
  • segment 0
  • gct 0
  • cls 0
  • duphold 0
  • structural variation 0
  • depth information 0
  • escherichia coli 0
  • schema 0
  • percent on target 0
  • pep 0
  • eigenstratdatabasetools 0
  • eklipse 0
  • na 0
  • circos 0
  • deletion 0
  • version 0
  • split by chromosome 0
  • custom 0
  • embl 0
  • genbank 0
  • swissprot 0
  • Streptococcus pyogenes 0
  • endogenous DNA 0
  • lint 0
  • partition histograms 0
  • postprocessgermlinecnvcalls 0
  • genomicsdbimport 0
  • condensedepthevidence 0
  • createsequencedictionary 0
  • polymorphic 0
  • createsomaticpanelofnormals 0
  • polymut 0
  • determinegermlinecontigploidy 0
  • duplication metrics 0
  • estimatelibrarycomplexity 0
  • filterintervals 0
  • filtervarianttranches 0
  • tranche filtering 0
  • gatherbqsrreports 0
  • genomicsdb 0
  • jointgenotyping 0
  • composestrtablefile 0
  • panelofnormalscreation 0
  • germline contig ploidy 0
  • germlinecnvcaller 0
  • germlinevariantsites 0
  • getpileupsumaries 0
  • readcountssummary 0
  • splice 0
  • indexfeaturefile 0
  • learnreadorientationmodel 0
  • readorientationartifacts 0
  • leftalignandtrimvariants 0
  • mergebamalignment 0
  • mutectstats 0
  • snvs 0
  • dragstr 0
  • short variant discovery 0
  • rust 0
  • targets 0
  • variant caller 0
  • somatic variant calling 0
  • germline variant calling 0
  • bacterial variant calling 0
  • target 0
  • bootstrapping 0
  • UShER 0
  • gamma 0
  • gene-calling 0
  • gangstr 0
  • export 0
  • antitarget 0
  • heattree 0
  • access 0
  • annotateintervals 0
  • combinegvcfs 0
  • cmseq 0
  • protein coding genes 0
  • variant quality score recalibration 0
  • vqsr 0
  • asereadcounter 0
  • bedtointervallist 0
  • calculatecontamination 0
  • cross-samplecontamination 0
  • getpileupsummaries 0
  • calibratedragstrmodel 0
  • cnnscorevariants 0
  • collectreadcounts 0
  • collectsvevidence 0
  • polymorphic sites 0
  • subtract 0
  • spliced 0
  • genetic sex 0
  • genomic intervals 0
  • microscopy 0
  • background_correction 0
  • contact 0
  • pretext 0
  • jpg 0
  • bmp 0
  • contact maps 0
  • gene finding 0
  • illumiation_correction 0
  • element 0
  • intervals coverage 0
  • trimBam 0
  • bamUtil 0
  • normal database 0
  • pmdtools 0
  • panel of normals 0
  • cutoff 0
  • haplotype purging 0
  • duplicate purging 0
  • false duplications 0
  • assembly curation 0
  • Haplotype purging 0
  • False duplications 0
  • Assembly curation 0
  • bamtools/split 0
  • yaml 0
  • quast 0
  • neighbour-joining 0
  • subsampling 0
  • porechop_abi 0
  • variant genetic 0
  • rhocall 0
  • csRNA-seq 0
  • mate-pair 0
  • liftovervcf 0
  • pcr 0
  • picard/renamesampleinvcf 0
  • sortvcf 0
  • deletions 0
  • insertions 0
  • tandem duplications 0
  • CoPRO 0
  • GRO-cap 0
  • PRO-cap 0
  • CAGE 0
  • NETCAGE 0
  • RAMPAGE 0
  • STRIPE-seq 0
  • scoring 0
  • PRO-seq 0
  • GRO-seq 0
  • genetic 0
  • deduping 0
  • smaller fastqs 0
  • clumping fastqs 0
  • exclude 0
  • variant identifiers 0
  • subset 0
  • indep 0
  • indep pairwise 0
  • recode 0
  • whole genome association 0
  • identifiers 0
  • long uncorrected reads 0
  • R 0
  • csi 0
  • grep 0
  • clusteridentifier 0
  • peak-caller 0
  • cut&tag 0
  • cut&run 0
  • chromatin 0
  • seacr 0
  • assembly-binning 0
  • bacphlip 0
  • applyvarcal 0
  • VQSR 0
  • variant recalibration 0
  • virulent 0
  • subseq 0
  • scramble 0
  • sertotype 0
  • interleave 0
  • temperate 0
  • seq 0
  • selection 0
  • random draw 0
  • pseudohaploid 0
  • pseudodiploid 0
  • freqsum 0
  • bam2seqz 0
  • gc_wiggle 0
  • induce 0
  • sex determination 0
  • cluster analysis 0
  • readgroup 0
  • bamstat 0
  • rtg-tools 0
  • bamtools/convert 0
  • strandedness 0
  • experiment 0
  • read_pairs 0
  • fragment_size 0
  • inner_distance 0
  • read distribution 0
  • sequence-based 0
  • mapping-based 0
  • mouse 0
  • integrity 0
  • rtg 0
  • rocplot 0
  • salsa 0
  • read pairs 0
  • salsa2 0
  • LCA 0
  • Ancestor 0
  • multimapper 0
  • flagstat 0
  • sambamba 0
  • amplicon 0
  • ampliconclip 0
  • calmd 0
  • faidx 0
  • insert size 0
  • repair 0
  • paired 0
  • hybrid-selection 0
  • phylogenetic composition 0
  • train 0
  • contour map 0
  • chunking 0
  • mass-spectroscopy 0
  • mcr-1 0
  • MD5 0
  • 128 bit 0
  • megahit 0
  • denovo 0
  • debruijn 0
  • daa 0
  • rma6 0
  • Neisseria meningitidis 0
  • k-mer frequency 0
  • 3D heat map 0
  • Merqury 0
  • maskfasta 0
  • jaccard 0
  • assembly evaluation 0
  • smudgeplot 0
  • ploidy 0
  • unionsum 0
  • metaphlan 0
  • methylation bias 0
  • mbias 0
  • assembler 0
  • de Bruijn 0
  • overlap 0
  • microrna 0
  • getfasta 0
  • target prediction 0
  • metagenome-assembled genomes 0
  • maxbin2 0
  • reference genome 0
  • functional genomics 0
  • adapter removal 0
  • collapsing 0
  • legionella 0
  • clinical 0
  • pneumophila 0
  • limma 0
  • Listeria monocytogenes 0
  • slopBed 0
  • lofreq/call 0
  • lofreq/filter 0
  • qualities 0
  • AMP 0
  • peptide prediction 0
  • bases 0
  • sgRNA 0
  • representations 0
  • CRISPR-Cas9 0
  • maximum-likelihood 0
  • rra 0
  • sizes 0
  • region 0
  • shiftBed 0
  • DNA damage 0
  • NGS 0
  • damage patterns 0
  • multinterval 0
  • overlapped bed 0
  • taxonomic assignment 0
  • mash/sketch 0
  • reduced 0
  • mitochondrial genome 0
  • genomecov 0
  • illumina datasets 0
  • select 0
  • tumor/normal 0
  • hla-typing 0
  • ILP 0
  • HLA-I 0
  • block-compressed 0
  • PCR/optical duplicates 0
  • flip 0
  • upper-triangular matrix 0
  • ligation junctions 0
  • pairtools 0
  • pairstools 0
  • restriction fragments 0
  • BCF 0
  • graph formats 0
  • paragraph 0
  • graphs 0
  • pbbam 0
  • pbmerge 0
  • subreads 0
  • pbp 0
  • pair-end 0
  • read 0
  • pedigrees 0
  • motif 0
  • ChIP-Seq 0
  • phantom peaks 0
  • prophage 0
  • identification 0
  • graph viz 0
  • graph unchopping 0
  • closest 0
  • contaminant 0
  • bamtobed 0
  • mosdepth 0
  • otu table 0
  • sorting 0
  • microsatellite instability 0
  • scan 0
  • mtnucratio 0
  • ratio 0
  • autozygosity 0
  • mitochondrial to nuclear ratio 0
  • bioinformatics tools 0
  • Beautiful stand-alone HTML report 0
  • GATK UnifiedGenotyper 0
  • SNP table 0
  • cancer genome 0
  • graph stats 0
  • somatic structural variations 0
  • mobile element insertions 0
  • sequencing summary 0
  • NextGenMap 0
  • ngm 0
  • Neisseria gonorrhoeae 0
  • gender 0
  • homozygosity 0
  • biallelic 0
  • graph construction 0
  • graph drawing 0
  • squeeze 0
  • odgi 0
  • combine graphs 0
  • taxonomic composition 0

removes unused references from header of sorted BAM/CRAM files.

01

bam versions

Filter out sequences by sequence header name(s)

01000

reads log versions

bbmap:

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

bcftools Haplotype-aware consequence caller

01010101

vcf tbi csi versions

reheader:

Haplotype-aware consequence caller

Reheader a VCF file

012301

vcf index versions

reheader:

Modify header of VCF/BCF files, change sample names.

Creates a sequence dictionary for a reference sequence.

01

reference_dict versions

picard:

Creates a sequence dictionary file (with ".dict" extension) from a reference sequence provided in FASTA format, which is required by many processing and analysis tools. The output file contains a header but no SAMRecords, and the header contains only sequence records.

Converts a PED file to VCF headers

01

output versions

rtgtools:

RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation

This module combines samtools and samblaster in order to use samblaster capability to filter or tag SAM files, with the advantage of maintaining both input and output in BAM format. Samblaster input must contain a sequence header: for this reason it has been piped with the "samtools view -h" command. Additional desired arguments for samtools can be passed using: options.args2 for the input bam file options.args3 for the output bam file

01

bam versions

Replace the header in the bam file with the header generated by the command. This command is much faster than replacing the header with a BAMโ†’SAMโ†’BAM conversion.

01

bam versions

samtools:

SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.

Dereplicate FASTX sequences, removing duplicate sequences and printing the number of identical sequences in the sequence header. Can dereplicate already dereplicated FASTA files, summing the numbers found in the headers.

01

fasta versions

seqfu:

DNA sequence utilities for FASTX files

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.

Rename sequence names in FASTQ or FASTA files.

01

sequences versions

seqtk:

Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. The seqtk rename command renames sequence names.

Reformats the header of PDB files with t-coffee

01

formatted_pdb versions

tcoffee:

A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.

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