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.

  • LAST 3
  • fasta 2
  • fastq 2
  • bam 1
  • genomics 1
  • metagenomics 1
  • alignment 1
  • cram 1
  • align 1
  • map 1
  • statistics 1
  • coverage 1
  • split 1
  • sentieon 1
  • rnaseq 1
  • QC 1
  • stats 1
  • complexity 1
  • dedup 1
  • diversity 1
  • mem 1
  • MAF 1
  • redundancy 1
  • duplication 1
  • multiqc 1
  • seqfu 1
  • n50 1
  • spliced 1
  • train 1
  • bioinformatics tools 1
  • Beautiful stand-alone HTML report 1
  • vcf 0
  • genome 0
  • index 0
  • reference 0
  • assembly 0
  • bed 0
  • gatk4 0
  • sort 0
  • sam 0
  • structural variants 0
  • variant calling 0
  • annotation 0
  • database 0
  • merge 0
  • filter 0
  • gff 0
  • bacteria 0
  • qc 0
  • variants 0
  • classification 0
  • classify 0
  • nanopore 0
  • quality control 0
  • download 0
  • gtf 0
  • cnv 0
  • MSA 0
  • k-mer 0
  • contamination 0
  • variant 0
  • taxonomy 0
  • taxonomic profiling 0
  • gfa 0
  • somatic 0
  • pacbio 0
  • convert 0
  • conversion 0
  • clustering 0
  • proteomics 0
  • quality 0
  • binning 0
  • count 0
  • copy number 0
  • ancient DNA 0
  • single-cell 0
  • VCF 0
  • imputation 0
  • bedtools 0
  • trimming 0
  • phylogeny 0
  • contigs 0
  • mags 0
  • build 0
  • graph 0
  • long reads 0
  • kmer 0
  • isoseq 0
  • gvcf 0
  • sv 0
  • bcftools 0
  • bisulfite 0
  • variation graph 0
  • reporting 0
  • bqsr 0
  • illumina 0
  • table 0
  • long-read 0
  • picard 0
  • indexing 0
  • wgs 0
  • databases 0
  • cna 0
  • consensus 0
  • bisulphite 0
  • methylseq 0
  • protein 0
  • methylation 0
  • compression 0
  • visualisation 0
  • serotype 0
  • phage 0
  • openms 0
  • metrics 0
  • tsv 0
  • imaging 0
  • demultiplex 0
  • 5mC 0
  • taxonomic classification 0
  • antimicrobial resistance 0
  • sequences 0
  • mapping 0
  • depth 0
  • bins 0
  • cluster 0
  • histogram 0
  • WGBS 0
  • scWGBS 0
  • pairs 0
  • searching 0
  • pangenome graph 0
  • structure 0
  • expression 0
  • aDNA 0
  • protein sequence 0
  • base quality score recalibration 0
  • amr 0
  • plot 0
  • markduplicates 0
  • haplotype 0
  • DNA methylation 0
  • neural network 0
  • matrix 0
  • palaeogenomics 0
  • archaeogenomics 0
  • repeat 0
  • mmseqs2 0
  • mappability 0
  • db 0
  • samtools 0
  • machine learning 0
  • iCLIP 0
  • checkm 0
  • genotype 0
  • annotate 0
  • bwa 0
  • damage 0
  • completeness 0
  • metagenome 0
  • filtering 0
  • virus 0
  • gzip 0
  • validation 0
  • transcript 0
  • biscuit 0
  • low-coverage 0
  • bcf 0
  • bisulfite sequencing 0
  • cooler 0
  • aligner 0
  • mag 0
  • spatial 0
  • blast 0
  • decompression 0
  • ncbi 0
  • newick 0
  • umi 0
  • glimpse 0
  • population genetics 0
  • bismark 0
  • gff3 0
  • hmmsearch 0
  • evaluation 0
  • gene 0
  • segmentation 0
  • mkref 0
  • peaks 0
  • msa 0
  • hmmer 0
  • seqkit 0
  • example 0
  • phasing 0
  • genotyping 0
  • ucsc 0
  • sequence 0
  • transcriptome 0
  • kraken2 0
  • germline 0
  • mitochondria 0
  • demultiplexing 0
  • differential 0
  • prokaryote 0
  • snp 0
  • feature 0
  • deduplication 0
  • mirna 0
  • antimicrobial resistance genes 0
  • single 0
  • plasmid 0
  • antimicrobial peptides 0
  • pangenome 0
  • splicing 0
  • json 0
  • multiple sequence alignment 0
  • cnvkit 0
  • scRNA-seq 0
  • prediction 0
  • low frequency variant calling 0
  • kmers 0
  • tumor-only 0
  • NCBI 0
  • duplicates 0
  • short-read 0
  • report 0
  • vsearch 0
  • bedGraph 0
  • svtk 0
  • isolates 0
  • amps 0
  • de novo 0
  • tabular 0
  • single cell 0
  • text 0
  • sourmash 0
  • call 0
  • FASTQ 0
  • fragment 0
  • csv 0
  • cat 0
  • concatenate 0
  • 3-letter genome 0
  • extract 0
  • ptr 0
  • indels 0
  • mutect2 0
  • microbiome 0
  • counts 0
  • query 0
  • view 0
  • clipping 0
  • coptr 0
  • deamination 0
  • mpileup 0
  • interval 0
  • riboseq 0
  • visualization 0
  • summary 0
  • antibiotic resistance 0
  • benchmark 0
  • detection 0
  • idXML 0
  • de novo assembly 0
  • arg 0
  • gridss 0
  • wxs 0
  • adapters 0
  • profiling 0
  • structural 0
  • profile 0
  • merging 0
  • kallisto 0
  • preprocessing 0
  • containment 0
  • deep learning 0
  • interval_list 0
  • rna 0
  • peak-calling 0
  • compare 0
  • ranking 0
  • genmod 0
  • bedgraph 0
  • enrichment 0
  • happy 0
  • read depth 0
  • HiFi 0
  • CLIP 0
  • hmmcopy 0
  • haplotypecaller 0
  • biosynthetic gene cluster 0
  • ccs 0
  • HMM 0
  • fastx 0
  • microarray 0
  • sequencing 0
  • mtDNA 0
  • snps 0
  • copy number alteration calling 0
  • hybrid capture sequencing 0
  • targeted sequencing 0
  • DNA sequencing 0
  • diamond 0
  • SV 0
  • miscoding lesions 0
  • palaeogenetics 0
  • archaeogenetics 0
  • sample 0
  • bigwig 0
  • bin 0
  • gsea 0
  • family 0
  • bgzip 0
  • genome assembler 0
  • hic 0
  • ganon 0
  • quantification 0
  • reference-free 0
  • compress 0
  • paf 0
  • ancestry 0
  • public datasets 0
  • microsatellite 0
  • fgbio 0
  • reads 0
  • ngscheckmate 0
  • matching 0
  • STR 0
  • phylogenetic placement 0
  • BGC 0
  • cut 0
  • circrna 0
  • malt 0
  • ont 0
  • image 0
  • umitools 0
  • abundance 0
  • DNA sequence 0
  • ampir 0
  • logratio 0
  • propr 0
  • bedpe 0
  • add 0
  • sketch 0
  • parsing 0
  • xeniumranger 0
  • telomere 0
  • normalization 0
  • retrotransposon 0
  • chunk 0
  • transcriptomics 0
  • ATAC-seq 0
  • resistance 0
  • isomir 0
  • fungi 0
  • pypgx 0
  • bcl2fastq 0
  • union 0
  • relatedness 0
  • hidden Markov model 0
  • quality trimming 0
  • atac-seq 0
  • fai 0
  • wig 0
  • bacterial 0
  • ataqv 0
  • somatic variants 0
  • transposons 0
  • chip-seq 0
  • rna_structure 0
  • intervals 0
  • RNA 0
  • converter 0
  • mzml 0
  • adapter trimming 0
  • highly_multiplexed_imaging 0
  • prokka 0
  • ambient RNA removal 0
  • panel 0
  • chromosome 0
  • fastk 0
  • genomes 0
  • mlst 0
  • PacBio 0
  • PCA 0
  • scores 0
  • uLTRA 0
  • rsem 0
  • survivor 0
  • popscle 0
  • gene expression 0
  • fingerprint 0
  • repeat expansion 0
  • UMI 0
  • comparisons 0
  • pseudoalignment 0
  • organelle 0
  • krona chart 0
  • entrez 0
  • complement 0
  • tabix 0
  • structural_variants 0
  • krona 0
  • typing 0
  • dictionary 0
  • remove 0
  • lineage 0
  • pangolin 0
  • covid 0
  • pan-genome 0
  • pairsam 0
  • replace 0
  • angsd 0
  • mcmicro 0
  • html 0
  • cfDNA 0
  • gatk4spark 0
  • image_analysis 0
  • dna 0
  • genotype-based deconvoltion 0
  • plink2 0
  • roh 0
  • insert 0
  • png 0
  • amplicon sequencing 0
  • notebook 0
  • fam 0
  • reports 0
  • bim 0
  • kraken 0
  • variant_calling 0
  • DRAMP 0
  • deeparg 0
  • cool 0
  • cut up 0
  • untar 0
  • hi-c 0
  • uncompress 0
  • unzip 0
  • zip 0
  • eukaryotes 0
  • shapeit 0
  • archiving 0
  • ligate 0
  • checkv 0
  • dump 0
  • amplify 0
  • polishing 0
  • benchmarking 0
  • macrel 0
  • score 0
  • distance 0
  • long_read 0
  • genome mining 0
  • genome assembly 0
  • identity 0
  • transcripts 0
  • host 0
  • bamtools 0
  • minimap2 0
  • lossless 0
  • prokaryotes 0
  • kinship 0
  • mkfastq 0
  • informative sites 0
  • observations 0
  • virulence 0
  • nucleotide 0
  • wastewater 0
  • clean 0
  • indel 0
  • miRNA 0
  • C to T 0
  • bwameth 0
  • amplicon sequences 0
  • fusion 0
  • chimeras 0
  • spaceranger 0
  • sylph 0
  • windowmasker 0
  • npz 0
  • subsample 0
  • mapper 0
  • das tool 0
  • arriba 0
  • guide tree 0
  • das_tool 0
  • combine 0
  • spark 0
  • neubi 0
  • fcs-gx 0
  • prefetch 0
  • cellranger 0
  • RNA-seq 0
  • pileup 0
  • CRISPR 0
  • aln 0
  • small indels 0
  • SNP 0
  • bakta 0
  • microbes 0
  • vrhyme 0
  • bracken 0
  • krakenuniq 0
  • barcode 0
  • primer 0
  • metamaps 0
  • pair 0
  • regression 0
  • interactive 0
  • krakentools 0
  • lift 0
  • interactions 0
  • serogroup 0
  • functional analysis 0
  • genetics 0
  • lofreq 0
  • reformat 0
  • taxids 0
  • gene set 0
  • dereplicate 0
  • repeats 0
  • haplogroups 0
  • ome-tif 0
  • MCMICRO 0
  • trancriptome 0
  • tama 0
  • gstama 0
  • mirdeep2 0
  • RNA sequencing 0
  • hla 0
  • gene set analysis 0
  • frame-shift correction 0
  • pigz 0
  • phase 0
  • standardise 0
  • smrnaseq 0
  • concordance 0
  • standardization 0
  • Pharmacogenetics 0
  • long-read sequencing 0
  • hlala 0
  • screen 0
  • refine 0
  • khmer 0
  • bustools 0
  • taxon name 0
  • zlib 0
  • differential expression 0
  • find 0
  • variation 0
  • polyA_tail 0
  • ampgram 0
  • maximum likelihood 0
  • hla_typing 0
  • iphop 0
  • instrain 0
  • ichorcna 0
  • amptransformer 0
  • minhash 0
  • mask 0
  • pharmacogenetics 0
  • mapcounter 0
  • sequence analysis 0
  • hlala_typing 0
  • leviosam2 0
  • graph layout 0
  • tree 0
  • proportionality 0
  • SimpleAF 0
  • scaffolding 0
  • image_processing 0
  • rtgtools 0
  • registration 0
  • junctions 0
  • mitochondrion 0
  • runs_of_homozygosity 0
  • polish 0
  • scaffold 0
  • comparison 0
  • collate 0
  • cnvnator 0
  • nucleotides 0
  • multiallelic 0
  • contig 0
  • small variants 0
  • rgfa 0
  • duplicate 0
  • Read depth 0
  • tnhaplotyper2 0
  • Duplication purging 0
  • purge duplications 0
  • bam2fq 0
  • dict 0
  • cleaning 0
  • sequenzautils 0
  • cancer genomics 0
  • split_kmers 0
  • snpsift 0
  • snpeff 0
  • effect prediction 0
  • FracMinHash sketch 0
  • shigella 0
  • trgt 0
  • switch 0
  • ancient dna 0
  • Streptococcus pneumoniae 0
  • transformation 0
  • fixmate 0
  • rename 0
  • vcflib 0
  • seqtk 0
  • salmonella 0
  • varcal 0
  • corrupted 0
  • vg 0
  • fusions 0
  • soft-clipped clusters 0
  • signature 0
  • reformatting 0
  • library 0
  • orf 0
  • anndata 0
  • pharokka 0
  • function 0
  • msisensor-pro 0
  • micro-satellite-scan 0
  • tumor 0
  • msi 0
  • instability 0
  • MSI 0
  • homoploymer 0
  • retrotransposons 0
  • long terminal repeat 0
  • long terminal retrotransposon 0
  • nextclade 0
  • kma 0
  • svdb 0
  • spatial_transcriptomics 0
  • resolve_bioscience 0
  • profiles 0
  • salmon 0
  • GC content 0
  • doublets 0
  • megan 0
  • checksum 0
  • mRNA 0
  • removal 0
  • gene labels 0
  • preseq 0
  • taxon tables 0
  • adapter 0
  • import 0
  • small genome 0
  • orthology 0
  • parallelized 0
  • variant pruning 0
  • bfiles 0
  • transcriptomic 0
  • screening 0
  • nacho 0
  • mudskipper 0
  • read-group 0
  • standardisation 0
  • ped 0
  • xz 0
  • nanostring 0
  • archive 0
  • COBS 0
  • k-mer index 0
  • bloom filter 0
  • GPU-accelerated 0
  • join 0
  • de novo assembler 0
  • otu tables 0
  • taxonomic profile 0
  • mash 0
  • ChIP-seq 0
  • awk 0
  • aggregate 0
  • evidence 0
  • demultiplexed reads 0
  • metagenomes 0
  • random forest 0
  • spatial_omics 0
  • regions 0
  • artic 0
  • interval list 0
  • heatmap 0
  • allele-specific 0
  • rna-seq 0
  • deseq2 0
  • blastp 0
  • panelofnormals 0
  • structural-variant calling 0
  • microbial 0
  • joint genotyping 0
  • NRPS 0
  • RiPP 0
  • proteome 0
  • version 0
  • gatk 0
  • settings 0
  • sra-tools 0
  • simulate 0
  • antibiotics 0
  • blastn 0
  • antismash 0
  • fasterq-dump 0
  • BAM 0
  • RNA-Seq 0
  • realignment 0
  • eido 0
  • secondary metabolites 0
  • concat 0
  • duplex 0
  • fetch 0
  • intersect 0
  • GEO 0
  • tbi 0
  • tab 0
  • metadata 0
  • norm 0
  • repeat_expansions 0
  • expansionhunterdenovo 0
  • metagenomic 0
  • microscopy 0
  • trim 0
  • identifier 0
  • normalize 0
  • UMIs 0
  • format 0
  • intersection 0
  • deconvolution 0
  • bayesian 0
  • samplesheet 0
  • validate 0
  • windows 0
  • eigenstrat 0
  • emboss 0
  • scatter 0
  • merge mate pairs 0
  • reads merging 0
  • short reads 0
  • xenograft 0
  • graft 0
  • reheader 0
  • unaligned 0
  • correction 0
  • filtermutectcalls 0
  • vdj 0
  • gwas 0
  • gem 0
  • CNV 0
  • MaltExtract 0
  • baf 0
  • HOPS 0
  • immunoprofiling 0
  • cnv calling 0
  • authentication 0
  • genomad 0
  • calling 0
  • allele 0
  • edit distance 0
  • parse 0
  • genome bins 0
  • estimation 0
  • eCLIP 0
  • cvnkit 0
  • single cells 0
  • recombination 0
  • Escherichia coli 0
  • sompy 0
  • genomecov 0
  • closest 0
  • peak picking 0
  • bamtobed 0
  • maskfasta 0
  • site frequency spectrum 0
  • rrna 0
  • ancestral alleles 0
  • quality assurnce 0
  • derived alleles 0
  • tnfilter 0
  • sorting 0
  • autozygosity 0
  • homozygosity 0
  • biallelic 0
  • getfasta 0
  • overlap 0
  • htseq 0
  • chunking 0
  • overlapped bed 0
  • simulation 0
  • hmmfetch 0
  • decompose 0
  • polya tail 0
  • fast5 0
  • multinterval 0
  • Read coverage histogram 0
  • qa 0
  • decompress 0
  • reverse complement 0
  • propd 0
  • array_cgh 0
  • transmembrane 0
  • vcf2bed 0
  • genome graph 0
  • tnseq 0
  • jaccard 0
  • decoy 0
  • shiftBed 0
  • topology 0
  • gprofiler2 0
  • rdtest 0
  • transform 0
  • variantcalling 0
  • deep variant 0
  • mutect 0
  • idx 0
  • sccmec 0
  • streptococcus 0
  • csi 0
  • spa 0
  • deduping 0
  • gaps 0
  • comparative genomics 0
  • introns 0
  • smaller fastqs 0
  • clumping fastqs 0
  • install 0
  • spatype 0
  • splice 0
  • joint-genotyping 0
  • genotypegvcf 0
  • background_correction 0
  • fracminhash sketch 0
  • BCF 0
  • spectral clustering 0
  • rdtest2vcf 0
  • rad 0
  • countsvtypes 0
  • cytosure 0
  • update header 0
  • vector 0
  • boxcox 0
  • baftest 0
  • gost 0
  • svtk/baftest 0
  • chromap 0
  • duplicate removal 0
  • short-read sequencing 0
  • sequence similarity 0
  • detecting svs 0
  • chromosome_visualization 0
  • structural variant 0
  • bam2fastx 0
  • bam2fastq 0
  • immcantation 0
  • airrseq 0
  • immunoinformatics 0
  • co-orthology 0
  • homology 0
  • region 0
  • crispr 0
  • sizes 0
  • vsearch/sort 0
  • umicollapse 0
  • postprocessing 0
  • cellpose 0
  • tblastn 0
  • extractunbinned 0
  • linkbins 0
  • mkvdjref 0
  • multiomics 0
  • ucsc/liftover 0
  • sintax 0
  • gtftogenepred 0
  • scRNA-Seq 0
  • usearch 0
  • refflat 0
  • long read alignment 0
  • pangenome-scale 0
  • all versus all 0
  • genepred 0
  • mashmap 0
  • bedtobigbed 0
  • wavefront 0
  • whamg 0
  • hifi 0
  • graph projection to vcf 0
  • bigbed 0
  • lua 0
  • upd 0
  • uniparental 0
  • disomy 0
  • snv 0
  • downsample 0
  • downsample bam 0
  • subsample bam 0
  • vcf2db 0
  • gemini 0
  • maf 0
  • compartments 0
  • construct 0
  • files 0
  • toml 0
  • cadd 0
  • vcfbreakmulti 0
  • uniq 0
  • deduplicate 0
  • domains 0
  • VCFtools 0
  • verifybamid 0
  • DNA contamination estimation 0
  • Assembly 0
  • wham 0
  • subtyping 0
  • clr 0
  • antibody capture 0
  • chromosomal rearrangements 0
  • bioawk 0
  • createreadcountpanelofnormals 0
  • copyratios 0
  • denoisereadcounts 0
  • readwriter 0
  • dnamodelapply 0
  • Mycobacterium tuberculosis 0
  • dnascope 0
  • antigen capture 0
  • unionBedGraphs 0
  • workflow_mode 0
  • subtract 0
  • slopBed 0
  • groupby 0
  • tnscope 0
  • bgen 0
  • bases 0
  • chloroplast 0
  • confidence 0
  • calder2 0
  • blat 0
  • alr 0
  • eucaryotes 0
  • workflow 0
  • bedgraphtobigwig 0
  • adna 0
  • copy-number 0
  • copy number analysis 0
  • gender determination 0
  • Salmonella enterica 0
  • copy number alterations 0
  • copy number variation 0
  • yahs 0
  • geo 0
  • sequencing adapters 0
  • mapad 0
  • transcroder 0
  • snakemake 0
  • c to t 0
  • element 0
  • sorted 0
  • cds 0
  • proteus 0
  • readproteingroups 0
  • eigenvectors 0
  • hicPCA 0
  • sliding 0
  • file manipulation 0
  • coding 0
  • illumiation_correction 0
  • assay 0
  • trimBam 0
  • tar 0
  • variant-calling 0
  • stardist 0
  • telseq 0
  • vsearch/dereplicate 0
  • vsearch/fastqfilter 0
  • fastqfilter 0
  • ATACseq 0
  • shift 0
  • ATACshift 0
  • setgt 0
  • jvarkit 0
  • translate 0
  • tarball 0
  • search engine 0
  • targz 0
  • installation 0
  • doCounts 0
  • bclconvert 0
  • nucBed 0
  • AT content 0
  • nucleotide content 0
  • elfasta 0
  • elprep 0
  • allele counts 0
  • controlstatistics 0
  • source tracking 0
  • emoji 0
  • poolseq 0
  • mass_error 0
  • nuclear contamination estimate 0
  • tag2tag 0
  • cgMLST 0
  • WGS 0
  • redundant 0
  • nanoq 0
  • Read filters 0
  • Read trimming 0
  • Read report 0
  • drug categorization 0
  • uniques 0
  • Illumina 0
  • functional 0
  • impute-info 0
  • tags 0
  • hashing-based deconvolution 0
  • rank 0
  • java 0
  • script 0
  • xml 0
  • svg 0
  • standard 0
  • haplotag 0
  • staging 0
  • Staging 0
  • http(s) 0
  • utility 0
  • HLA 0
  • microRNA 0
  • quality_control 0
  • post Post-processing 0
  • featuretable 0
  • patterns 0
  • identity-by-descent 0
  • decomposeblocksub 0
  • block substitutions 0
  • pdb 0
  • run 0
  • updatedata 0
  • chip 0
  • partitioning 0
  • malformed 0
  • fix 0
  • paired reads re-pairing 0
  • regex 0
  • doublet 0
  • admixture 0
  • Immune Deconvolution 0
  • Bioinformatics Tools 0
  • Computational Immunology 0
  • catpack 0
  • prepare 0
  • mzML 0
  • taxonomic composition 0
  • antimicrobial reistance 0
  • contiguate 0
  • CRISPRi 0
  • 16S 0
  • hhsuite 0
  • hmmpress 0
  • adapterremoval 0
  • reference panels 0
  • doublet_detection 0
  • model 0
  • barcodes 0
  • subsetting 0
  • logFC 0
  • significance statistic 0
  • p-value 0
  • scvi 0
  • solo 0
  • import segmentation 0
  • nuclear segmentation 0
  • cell segmentation 0
  • relabel 0
  • resegment 0
  • morphology 0
  • hostile 0
  • mgi 0
  • decontamination 0
  • human removal 0
  • metagenome assembler 0
  • AMPs 0
  • antimicrobial peptide prediction 0
  • scanpy 0
  • amp 0
  • plotting 0
  • regtools 0
  • leafcutter 0
  • Staphylococcus aureus 0
  • affy 0
  • recovery 0
  • extraction 0
  • mass spectrometry 0
  • parallel 0
  • association 0
  • genotype likelihood 0
  • collapse 0
  • liftover 0
  • probabilistic realignment 0
  • cell_type_identification 0
  • cell_phenotyping 0
  • machine_learning 0
  • bacphlip 0
  • clahe 0
  • refresh 0
  • GWAS 0
  • hwe equilibrium 0
  • case/control 0
  • virulent 0
  • associations 0
  • spatial_neighborhoods 0
  • scimap 0
  • Bayesian 0
  • structural-variants 0
  • omics 0
  • biological activity 0
  • temperate 0
  • prior knowledge 0
  • tag 0
  • cell_barcodes 0
  • reference-independent 0
  • hwe statistics 0
  • go 0
  • r 0
  • bamUtil 0
  • plastid 0
  • resfinder 0
  • resistance genes 0
  • raw 0
  • mgf 0
  • parquet 0
  • parser 0
  • dbsnp 0
  • standardize 0
  • bamtools/split 0
  • quarto 0
  • python 0
  • coexpression 0
  • hardy-weinberg 0
  • correlation 0
  • corpcor 0
  • signatures 0
  • phylogenetics 0
  • minimum_evolution 0
  • distance-based 0
  • nucleotide sequence 0
  • homologs 0
  • yaml 0
  • multi-tool 0
  • predict 0
  • bamtools/convert 0
  • mouse 0
  • mygene 0
  • lifestyle 0
  • sage 0
  • post mortem damage 0
  • genotype-based demultiplexing 0
  • donor deconvolution 0
  • cellsnp 0
  • trimfq 0
  • vcflib/vcffixup 0
  • AC/NS/AF 0
  • Pacbio 0
  • guidetree 0
  • bwamem2 0
  • bwameme 0
  • grabix 0
  • ribosomal 0
  • 10x 0
  • atlas 0
  • droplet based single cells 0
  • regulatory network 0
  • mkarv 0
  • transcription factors 0
  • paraphase 0
  • selector 0
  • cram-size 0
  • size 0
  • quality check 0
  • realign 0
  • circular 0
  • spot 0
  • orthogroup 0
  • orthologs 0
  • lexogen 0
  • busco 0
  • autofluorescence 0
  • translation 0
  • pile up 0
  • cycif 0
  • background 0
  • single-stranded 0
  • ancientDNA 0
  • authentict 0
  • nanopore sequencing 0
  • rna velocity 0
  • cobra 0
  • extension 0
  • grea 0
  • read group 0
  • functional enrichment 0
  • paired reads merging 0
  • InterProScan 0
  • overlap-based merging 0
  • check 0
  • bias 0
  • hamming-distance 0
  • hashing-based deconvoltion 0
  • gnu 0
  • coreutils 0
  • generic 0
  • transposable element 0
  • retrieval 0
  • ATLAS 0
  • sequencing_bias 0
  • MMseqs2 0
  • hash sketch 0
  • CRAM 0
  • polymut 0
  • NGS 0
  • qualities 0
  • AMP 0
  • peptide prediction 0
  • functional genomics 0
  • sgRNA 0
  • CRISPR-Cas9 0
  • maximum-likelihood 0
  • rra 0
  • vqsr 0
  • variant quality score recalibration 0
  • annotateintervals 0
  • DNA damage 0
  • damage patterns 0
  • lofreq/call 0
  • targets 0
  • estimate 0
  • taxonomic assignment 0
  • heattree 0
  • mash/sketch 0
  • gangstr 0
  • reduced 0
  • representations 0
  • maxbin2 0
  • gene-calling 0
  • metagenome-assembled genomes 0
  • gamma 0
  • lofreq/filter 0
  • asereadcounter 0
  • UShER 0
  • cnnscorevariants 0
  • Klebsiella 0
  • pneumoniae 0
  • condensedepthevidence 0
  • kegg 0
  • kofamscan 0
  • dragstr 0
  • combining 0
  • composestrtablefile 0
  • short variant discovery 0
  • combinegvcfs 0
  • collectsvevidence 0
  • collectreadcounts 0
  • calibratedragstrmodel 0
  • bedtointervallist 0
  • reorder 0
  • adapter removal 0
  • collapsing 0
  • getpileupsummaries 0
  • legionella 0
  • clinical 0
  • pneumophila 0
  • cross-samplecontamination 0
  • calculatecontamination 0
  • limma 0
  • Listeria monocytogenes 0
  • mass-spectroscopy 0
  • mcr-1 0
  • k-mer counting 0
  • consensus sequence 0
  • mitochondrial genome 0
  • reference genome 0
  • generate 0
  • single molecule 0
  • mosdepth 0
  • otu table 0
  • zipperbams 0
  • ubam 0
  • unmapped 0
  • groupreads 0
  • duplexumi 0
  • microsatellite instability 0
  • scan 0
  • random 0
  • mtnucratio 0
  • ratio 0
  • mitochondrial to nuclear ratio 0
  • GATK UnifiedGenotyper 0
  • SNP table 0
  • contaminant 0
  • public 0
  • cancer genome 0
  • somatic structural variations 0
  • mobile element insertions 0
  • sequencing summary 0
  • target prediction 0
  • microrna 0
  • bootstrapping 0
  • contour map 0
  • MD5 0
  • 128 bit 0
  • megahit 0
  • denovo 0
  • debruijn 0
  • daa 0
  • rma6 0
  • Neisseria meningitidis 0
  • bacterial variant calling 0
  • k-mer frequency 0
  • germline variant calling 0
  • 3D heat map 0
  • Merqury 0
  • lint 0
  • somatic variant calling 0
  • assembly evaluation 0
  • smudgeplot 0
  • ploidy 0
  • unionsum 0
  • metaphlan 0
  • variant caller 0
  • methylation bias 0
  • mbias 0
  • rust 0
  • fq 0
  • assembler 0
  • de Bruijn 0
  • effective genome size 0
  • createsequencedictionary 0
  • ngm 0
  • extract_variants 0
  • svcluster 0
  • svannotate 0
  • gstama/polyacleanup 0
  • GTDB taxonomy 0
  • splitintervals 0
  • genome taxonomy database 0
  • archaea 0
  • splitcram 0
  • gunc 0
  • gunzip 0
  • site depth 0
  • gvcftools 0
  • extractvariants 0
  • variantfiltration 0
  • shiftintervals 0
  • abricate 0
  • amrfinderplus 0
  • fARGene 0
  • rgi 0
  • ibd 0
  • hbd 0
  • beagle 0
  • mitochondrial 0
  • shiftfasta 0
  • shiftchain 0
  • selectvariants 0
  • Haemophilus influenzae 0
  • gstama/merge 0
  • TAMA 0
  • revert 0
  • genome profile 0
  • Mykrobe 0
  • genome summary 0
  • genome manipulation 0
  • genome statistics 0
  • Salmonella Typhi 0
  • repeat content 0
  • genome heterozygosity 0
  • gget 0
  • low coverage 0
  • genome size 0
  • models 0
  • compound 0
  • Sample 0
  • gene model 0
  • Haplotypes 0
  • Imputation 0
  • joint-variant-calling 0
  • GNU 0
  • merge compare 0
  • genomes on a tree 0
  • bgc 0
  • file parsing 0
  • txt 0
  • gawk 0
  • tama_collapse.py 0
  • variantrecalibrator 0
  • recalibration model 0
  • haplotype resolution 0
  • reblockgvcf 0
  • digital normalization 0
  • jasminesv 0
  • pixel_classification 0
  • probability_maps 0
  • germline contig ploidy 0
  • population genomics 0
  • interproscan 0
  • panelofnormalscreation 0
  • genomic islands 0
  • insertion 0
  • jointgenotyping 0
  • genomicsdbimport 0
  • genomicsdb 0
  • gatherbqsrreports 0
  • jasmine 0
  • multicut 0
  • Python 0
  • Jupyter 0
  • jupytext 0
  • papermill 0
  • tranche filtering 0
  • filtervarianttranches 0
  • filterintervals 0
  • estimatelibrarycomplexity 0
  • duplication metrics 0
  • kallisto/index 0
  • quant 0
  • determinegermlinecontigploidy 0
  • createsomaticpanelofnormals 0
  • pixel classification 0
  • genome browser 0
  • printsvevidence 0
  • amino acid 0
  • printreads 0
  • preprocessintervals 0
  • postprocessgermlinecnvcalls 0
  • snvs 0
  • mutectstats 0
  • gccounter 0
  • mergebamalignment 0
  • readcounter 0
  • leftalignandtrimvariants 0
  • readorientationartifacts 0
  • learnreadorientationmodel 0
  • HMMER 0
  • indexfeaturefile 0
  • js 0
  • readcountssummary 0
  • Hidden Markov Model 0
  • hmtnote 0
  • annotations 0
  • getpileupsumaries 0
  • pos 0
  • haemophilus 0
  • germlinevariantsites 0
  • germlinecnvcaller 0
  • panel_of_normals 0
  • IDR 0
  • igv 0
  • igv.js 0
  • NextGenMap 0
  • Neisseria gonorrhoeae 0
  • polymorphic 0
  • peak-caller 0
  • gct 0
  • cls 0
  • faidx 0
  • insert size 0
  • repair 0
  • paired 0
  • read pairs 0
  • readgroup 0
  • na 0
  • scramble 0
  • cluster analysis 0
  • clusteridentifier 0
  • cut&tag 0
  • cutesv 0
  • cut&run 0
  • chromatin 0
  • seacr 0
  • custom 0
  • assembly-binning 0
  • applyvarcal 0
  • Cores 0
  • VQSR 0
  • variant recalibration 0
  • Segmentation 0
  • subseq 0
  • grep 0
  • sequence headers 0
  • calmd 0
  • ampliconclip 0
  • sertotype 0
  • integrity 0
  • R 0
  • corrrelation 0
  • bamstat 0
  • strandedness 0
  • experiment 0
  • read_pairs 0
  • fragment_size 0
  • inner_distance 0
  • track 0
  • read distribution 0
  • sequence-based 0
  • mapping-based 0
  • rtg 0
  • amplicon 0
  • pedfilter 0
  • rocplot 0
  • paired-end 0
  • rtg-tools 0
  • pcr duplicates 0
  • salsa 0
  • salsa2 0
  • LCA 0
  • Ancestor 0
  • multimapper 0
  • flagstat 0
  • sambamba 0
  • duplicate marking 0
  • TMA dearray 0
  • UNet 0
  • long uncorrected reads 0
  • dist 0
  • boxplot 0
  • density 0
  • features 0
  • sliding window 0
  • partition histograms 0
  • gfastats 0
  • SMN1 0
  • SMN2 0
  • POA 0
  • sniffles 0
  • core 0
  • snippy 0
  • target 0
  • shinyngs 0
  • export 0
  • antitarget 0
  • dbnsfp 0
  • predictions 0
  • access 0
  • SNPs 0
  • invariant 0
  • constant 0
  • cmseq 0
  • protein coding genes 0
  • rRNA 0
  • ribosomal RNA 0
  • polymorphic sites 0
  • exploratory 0
  • concoct 0
  • interleave 0
  • gc_wiggle 0
  • mcool 0
  • genomic bins 0
  • header 0
  • seq 0
  • makebins 0
  • selection 0
  • random draw 0
  • pseudohaploid 0
  • pseudodiploid 0
  • freqsum 0
  • enzyme 0
  • bam2seqz 0
  • induce 0
  • 256 bit 0
  • digest 0
  • sex determination 0
  • genetic sex 0
  • relative coverage 0
  • cload 0
  • cooler/balance 0
  • subcontigs 0
  • rare variants 0
  • error 0
  • nucleotide composition 0
  • de-novo 0
  • longread 0
  • sha256 0
  • rhocall 0
  • subsampling 0
  • gender 0
  • identification 0
  • pbbam 0
  • pbmerge 0
  • subreads 0
  • pbp 0
  • pair-end 0
  • read 0
  • pedigrees 0
  • cache 0
  • motif 0
  • ChIP-Seq 0
  • phantom peaks 0
  • prophage 0
  • illumina datasets 0
  • paragraph 0
  • phylogenetic composition 0
  • percent on target 0
  • endogenous DNA 0
  • Streptococcus pyogenes 0
  • swissprot 0
  • hybrid-selection 0
  • mate-pair 0
  • liftovervcf 0
  • pcr 0
  • picard/renamesampleinvcf 0
  • sortvcf 0
  • deletions 0
  • insertions 0
  • graphs 0
  • str 0
  • CoPRO 0
  • tumor/normal 0
  • ENA 0
  • SRA 0
  • graph construction 0
  • graph drawing 0
  • ANI 0
  • squeeze 0
  • odgi 0
  • combine graphs 0
  • graph stats 0
  • graph unchopping 0
  • graph formats 0
  • graph viz 0
  • hla-typing 0
  • faqcs 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
  • select 0
  • ARGs 0
  • antibiotic resistance genes 0
  • tandem duplications 0
  • GRO-cap 0
  • neighbour-joining 0
  • structural variation 0
  • jpg 0
  • bmp 0
  • contact maps 0
  • gene finding 0
  • PEP 0
  • intervals coverage 0
  • escherichia coli 0
  • depth information 0
  • genomic intervals 0
  • normal database 0
  • panel of normals 0
  • cutoff 0
  • haplotype purging 0
  • contact 0
  • duplicate purging 0
  • false duplications 0
  • assembly curation 0
  • Haplotype purging 0
  • duphold 0
  • False duplications 0
  • Assembly curation 0
  • segment 0
  • blastx 0
  • purging 0
  • quast 0
  • cumulative coverage 0
  • scatterplot 0
  • pretext 0
  • schema 0
  • PRO-cap 0
  • split by chromosome 0
  • CAGE 0
  • NETCAGE 0
  • RAMPAGE 0
  • csRNA-seq 0
  • STRIPE-seq 0
  • PRO-seq 0
  • GRO-seq 0
  • genetic 0
  • genbank 0
  • embl 0
  • exclude 0
  • variant identifiers 0
  • subset 0
  • pep 0
  • deletion 0
  • indep 0
  • circos 0
  • indep pairwise 0
  • recode 0
  • whole genome association 0
  • eklipse 0
  • identifiers 0
  • scoring 0
  • eigenstratdatabasetools 0
  • variant genetic 0
  • pmdtools 0
  • porechop_abi 0
  • hmmscan 0

Assessment of duplication rates in RNA-Seq datasets

0101

scatter2d boxplot hist dupmatrix intercept_slope multiqc session_info versions

Aligns query sequences to target sequences indexed with lastdb

0120

maf multiqc 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.

Aggregate results from bioinformatics analyses across many samples into a single report

000000

report data plots versions

multiqc:

MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.

Generate summary reports with raw data for Nonpareil NPO curves, including MultiQC compatible JSON/TSV files

01

json tsv csv pdf versions

nonpareil:

Estimate average coverage and create curves for metagenomic datasets

Runs the sentieon tool LocusCollector followed by Dedup. LocusCollector collects read information that is used by Dedup which in turn marks or removes duplicate reads.

0120101

cram crai bam bai score metrics metrics_multiqc_tsv versions

sentieon:

Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.

Statistics for FASTA or FASTQ files

01

stats multiqc versions

seqfu:

Cross-platform compiled suite of tools to manipulate and inspect FASTA and FASTQ files

Click here to trigger an update.