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.

  • complexity 7
  • metagenomics 5
  • statistics 5
  • coverage 5
  • diversity 4
  • redundancy 4
  • fasta 3
  • windowmasker 3
  • gatk4 2
  • visualisation 2
  • interval 2
  • smrnaseq 2
  • library 2
  • preseq 2
  • reporting 1
  • QC 1
  • cluster 1
  • blast 1
  • mirna 1
  • microRNA 1
  • multiqc 1
  • composestrtablefile 1
  • dragstr 1
  • duplication metrics 1
  • estimatelibrarycomplexity 1
  • bam 0
  • vcf 0
  • fastq 0
  • genomics 0
  • genome 0
  • index 0
  • reference 0
  • alignment 0
  • assembly 0
  • bed 0
  • cram 0
  • sam 0
  • sort 0
  • structural variants 0
  • variant calling 0
  • annotation 0
  • database 0
  • align 0
  • merge 0
  • filter 0
  • gff 0
  • bacteria 0
  • map 0
  • qc 0
  • variants 0
  • quality control 0
  • classify 0
  • classification 0
  • gtf 0
  • download 0
  • cnv 0
  • nanopore 0
  • split 0
  • taxonomic profiling 0
  • variant 0
  • gfa 0
  • k-mer 0
  • MSA 0
  • contamination 0
  • pacbio 0
  • somatic 0
  • taxonomy 0
  • sentieon 0
  • convert 0
  • conversion 0
  • quality 0
  • binning 0
  • proteomics 0
  • count 0
  • clustering 0
  • VCF 0
  • ancient DNA 0
  • single-cell 0
  • copy number 0
  • phylogeny 0
  • contigs 0
  • bedtools 0
  • imputation 0
  • bcftools 0
  • bisulfite 0
  • graph 0
  • isoseq 0
  • long reads 0
  • mags 0
  • gvcf 0
  • trimming 0
  • sv 0
  • variation graph 0
  • build 0
  • illumina 0
  • compression 0
  • picard 0
  • cna 0
  • bqsr 0
  • methylseq 0
  • kmer 0
  • rnaseq 0
  • protein 0
  • consensus 0
  • indexing 0
  • databases 0
  • wgs 0
  • table 0
  • bisulphite 0
  • methylation 0
  • stats 0
  • 5mC 0
  • long-read 0
  • phage 0
  • sequences 0
  • metrics 0
  • demultiplex 0
  • taxonomic classification 0
  • serotype 0
  • imaging 0
  • openms 0
  • tsv 0
  • antimicrobial resistance 0
  • mapping 0
  • searching 0
  • matrix 0
  • histogram 0
  • structure 0
  • neural network 0
  • markduplicates 0
  • DNA methylation 0
  • plot 0
  • depth 0
  • amr 0
  • scWGBS 0
  • expression 0
  • WGBS 0
  • base quality score recalibration 0
  • bins 0
  • pangenome graph 0
  • protein sequence 0
  • aDNA 0
  • haplotype 0
  • pairs 0
  • damage 0
  • filtering 0
  • archaeogenomics 0
  • machine learning 0
  • bcf 0
  • palaeogenomics 0
  • mmseqs2 0
  • transcript 0
  • samtools 0
  • virus 0
  • low-coverage 0
  • validation 0
  • bisulfite sequencing 0
  • biscuit 0
  • bwa 0
  • iCLIP 0
  • completeness 0
  • metagenome 0
  • checkm 0
  • db 0
  • cooler 0
  • repeat 0
  • annotate 0
  • mappability 0
  • LAST 0
  • aligner 0
  • genotype 0
  • genotyping 0
  • hmmsearch 0
  • mag 0
  • bismark 0
  • gff3 0
  • dedup 0
  • population genetics 0
  • mkref 0
  • example 0
  • umi 0
  • segmentation 0
  • gzip 0
  • ncbi 0
  • ucsc 0
  • kraken2 0
  • transcriptome 0
  • phasing 0
  • germline 0
  • sequence 0
  • newick 0
  • seqkit 0
  • peaks 0
  • glimpse 0
  • spatial 0
  • gene 0
  • decompression 0
  • msa 0
  • evaluation 0
  • antimicrobial peptides 0
  • NCBI 0
  • vsearch 0
  • mitochondria 0
  • low frequency variant calling 0
  • single 0
  • short-read 0
  • feature 0
  • tumor-only 0
  • bedGraph 0
  • differential 0
  • scRNA-seq 0
  • duplicates 0
  • deduplication 0
  • demultiplexing 0
  • kmers 0
  • prediction 0
  • splicing 0
  • antimicrobial resistance genes 0
  • hmmer 0
  • report 0
  • prokaryote 0
  • snp 0
  • pangenome 0
  • cnvkit 0
  • json 0
  • plasmid 0
  • multiple sequence alignment 0
  • 3-letter genome 0
  • kallisto 0
  • concatenate 0
  • tabular 0
  • amps 0
  • single cell 0
  • mutect2 0
  • counts 0
  • cat 0
  • benchmark 0
  • idXML 0
  • antibiotic resistance 0
  • gridss 0
  • text 0
  • arg 0
  • deamination 0
  • indels 0
  • de novo 0
  • visualization 0
  • MAF 0
  • csv 0
  • summary 0
  • view 0
  • query 0
  • mem 0
  • wxs 0
  • mpileup 0
  • extract 0
  • ptr 0
  • sourmash 0
  • coptr 0
  • riboseq 0
  • detection 0
  • merging 0
  • isolates 0
  • call 0
  • profiling 0
  • de novo assembly 0
  • clipping 0
  • adapters 0
  • svtk 0
  • microbiome 0
  • fragment 0
  • pypgx 0
  • read depth 0
  • compress 0
  • gsea 0
  • cut 0
  • CLIP 0
  • quantification 0
  • isomir 0
  • ngscheckmate 0
  • paf 0
  • matching 0
  • retrotransposon 0
  • reads 0
  • microsatellite 0
  • hic 0
  • xeniumranger 0
  • reference-free 0
  • ccs 0
  • telomere 0
  • FASTQ 0
  • umitools 0
  • phylogenetic placement 0
  • ont 0
  • STR 0
  • DNA sequencing 0
  • enrichment 0
  • fgbio 0
  • sequencing 0
  • sample 0
  • genome assembler 0
  • hybrid capture sequencing 0
  • compare 0
  • ganon 0
  • peak-calling 0
  • ranking 0
  • interval_list 0
  • haplotypecaller 0
  • bgzip 0
  • genmod 0
  • fastx 0
  • targeted sequencing 0
  • public datasets 0
  • miscoding lesions 0
  • HiFi 0
  • palaeogenetics 0
  • preprocessing 0
  • archaeogenetics 0
  • deep learning 0
  • family 0
  • propr 0
  • bedgraph 0
  • hmmcopy 0
  • happy 0
  • SV 0
  • bin 0
  • bigwig 0
  • profile 0
  • structural 0
  • diamond 0
  • copy number alteration calling 0
  • logratio 0
  • snps 0
  • mtDNA 0
  • circrna 0
  • containment 0
  • microarray 0
  • add 0
  • DNA sequence 0
  • abundance 0
  • ancestry 0
  • BGC 0
  • resistance 0
  • chunk 0
  • parsing 0
  • bcl2fastq 0
  • malt 0
  • normalization 0
  • ATAC-seq 0
  • sketch 0
  • ampir 0
  • biosynthetic gene cluster 0
  • union 0
  • fungi 0
  • eukaryotes 0
  • host 0
  • kinship 0
  • informative sites 0
  • typing 0
  • clean 0
  • complement 0
  • entrez 0
  • fai 0
  • PacBio 0
  • rsem 0
  • duplication 0
  • amplicon sequences 0
  • bamtools 0
  • DRAMP 0
  • vrhyme 0
  • plink2 0
  • spaceranger 0
  • fastk 0
  • miRNA 0
  • identity 0
  • HMM 0
  • relatedness 0
  • variant_calling 0
  • notebook 0
  • fingerprint 0
  • PCA 0
  • amplicon sequencing 0
  • combine 0
  • comparisons 0
  • bacterial 0
  • chromosome 0
  • dna 0
  • chimeras 0
  • virulence 0
  • benchmarking 0
  • arriba 0
  • fusion 0
  • fam 0
  • atac-seq 0
  • cfDNA 0
  • transposons 0
  • bakta 0
  • pileup 0
  • pairsam 0
  • genotype-based deconvoltion 0
  • prokaryotes 0
  • archiving 0
  • zip 0
  • roh 0
  • RNA 0
  • unzip 0
  • uncompress 0
  • indel 0
  • replace 0
  • score 0
  • quality trimming 0
  • spark 0
  • prokka 0
  • RNA-seq 0
  • insert 0
  • rna_structure 0
  • transcriptomics 0
  • untar 0
  • remove 0
  • popscle 0
  • long_read 0
  • wastewater 0
  • intervals 0
  • structural_variants 0
  • pan-genome 0
  • covid 0
  • converter 0
  • UMI 0
  • pangolin 0
  • lineage 0
  • npz 0
  • genome mining 0
  • uLTRA 0
  • ambient RNA removal 0
  • genome assembly 0
  • ligate 0
  • minimap2 0
  • subsample 0
  • dictionary 0
  • SNP 0
  • tabix 0
  • survivor 0
  • adapter trimming 0
  • transcripts 0
  • reports 0
  • amplify 0
  • krona chart 0
  • CRISPR 0
  • image 0
  • cool 0
  • somatic variants 0
  • nucleotide 0
  • dump 0
  • mzml 0
  • repeat expansion 0
  • gatk4spark 0
  • cut up 0
  • hi-c 0
  • bedpe 0
  • prefetch 0
  • mapper 0
  • fcs-gx 0
  • observations 0
  • image_analysis 0
  • mkfastq 0
  • macrel 0
  • bwameth 0
  • guide tree 0
  • chip-seq 0
  • wig 0
  • png 0
  • rna 0
  • checkv 0
  • neubi 0
  • polishing 0
  • mlst 0
  • panel 0
  • microbes 0
  • kraken 0
  • ataqv 0
  • angsd 0
  • small indels 0
  • gene expression 0
  • shapeit 0
  • cellranger 0
  • html 0
  • bim 0
  • C to T 0
  • deeparg 0
  • bracken 0
  • das_tool 0
  • lossless 0
  • genomes 0
  • organelle 0
  • das tool 0
  • mcmicro 0
  • krona 0
  • pseudoalignment 0
  • highly_multiplexed_imaging 0
  • aln 0
  • scores 0
  • functional analysis 0
  • gem 0
  • nucleotides 0
  • tree 0
  • tnhaplotyper2 0
  • k-mer index 0
  • minhash 0
  • iphop 0
  • genetics 0
  • polyA_tail 0
  • genomad 0
  • mash 0
  • ChIP-seq 0
  • multiallelic 0
  • read-group 0
  • small variants 0
  • simulate 0
  • cnvnator 0
  • rgfa 0
  • demultiplexed reads 0
  • refine 0
  • maximum likelihood 0
  • COBS 0
  • distance 0
  • interactions 0
  • comparison 0
  • baf 0
  • amptransformer 0
  • intersect 0
  • tbi 0
  • ampgram 0
  • registration 0
  • GC content 0
  • concat 0
  • bustools 0
  • variation 0
  • differential expression 0
  • xz 0
  • khmer 0
  • mitochondrion 0
  • proportionality 0
  • profiles 0
  • resolve_bioscience 0
  • megan 0
  • spatial_transcriptomics 0
  • zlib 0
  • archive 0
  • taxon name 0
  • taxids 0
  • nextclade 0
  • regression 0
  • mudskipper 0
  • screen 0
  • checksum 0
  • aggregate 0
  • concordance 0
  • ped 0
  • hla 0
  • primer 0
  • ichorcna 0
  • salmon 0
  • orthology 0
  • haplogroups 0
  • parallelized 0
  • tumor 0
  • micro-satellite-scan 0
  • graft 0
  • allele 0
  • msisensor-pro 0
  • hlala 0
  • barcode 0
  • hla_typing 0
  • retrotransposons 0
  • hlala_typing 0
  • xenograft 0
  • mapcounter 0
  • long terminal repeat 0
  • pair 0
  • graph layout 0
  • mask 0
  • interactive 0
  • kma 0
  • long terminal retrotransposon 0
  • krakenuniq 0
  • vg 0
  • gwas 0
  • SimpleAF 0
  • trim 0
  • krakentools 0
  • metamaps 0
  • hidden Markov model 0
  • bloom filter 0
  • lift 0
  • leviosam2 0
  • homoploymer 0
  • instrain 0
  • phase 0
  • gene set analysis 0
  • vcflib 0
  • gene set 0
  • GPU-accelerated 0
  • transcriptomic 0
  • msi 0
  • RNA-Seq 0
  • reformatting 0
  • artic 0
  • pharokka 0
  • function 0
  • gstama 0
  • orf 0
  • removal 0
  • trancriptome 0
  • MSI 0
  • lofreq 0
  • instability 0
  • serogroup 0
  • tama 0
  • taxon tables 0
  • gatk 0
  • snpeff 0
  • join 0
  • validate 0
  • samplesheet 0
  • format 0
  • eido 0
  • pharmacogenetics 0
  • scaffolding 0
  • cancer genomics 0
  • snpsift 0
  • effect prediction 0
  • eigenstrat 0
  • blastp 0
  • deseq2 0
  • rna-seq 0
  • doublets 0
  • awk 0
  • anndata 0
  • heatmap 0
  • regions 0
  • bam2fq 0
  • rtgtools 0
  • sequence analysis 0
  • random forest 0
  • signature 0
  • GEO 0
  • mirdeep2 0
  • RNA sequencing 0
  • metagenomic 0
  • identifier 0
  • runs_of_homozygosity 0
  • expansionhunterdenovo 0
  • repeat_expansions 0
  • intersection 0
  • long-read sequencing 0
  • windows 0
  • metadata 0
  • MaltExtract 0
  • tab 0
  • FracMinHash sketch 0
  • junctions 0
  • Pharmacogenetics 0
  • secondary metabolites 0
  • frame-shift correction 0
  • spatial_omics 0
  • BAM 0
  • polish 0
  • estimation 0
  • vdj 0
  • authentication 0
  • cnv calling 0
  • varcal 0
  • ancient dna 0
  • CNV 0
  • Streptococcus pneumoniae 0
  • cvnkit 0
  • salmonella 0
  • single cells 0
  • fusions 0
  • seqtk 0
  • recombination 0
  • genome bins 0
  • edit distance 0
  • eCLIP 0
  • rename 0
  • sequenzautils 0
  • parse 0
  • transformation 0
  • calling 0
  • immunoprofiling 0
  • metagenomes 0
  • sra-tools 0
  • blastn 0
  • collate 0
  • dict 0
  • proteome 0
  • fixmate 0
  • structural-variant calling 0
  • HOPS 0
  • gene labels 0
  • fasterq-dump 0
  • settings 0
  • mRNA 0
  • screening 0
  • cleaning 0
  • correction 0
  • trgt 0
  • soft-clipped clusters 0
  • shigella 0
  • corrupted 0
  • switch 0
  • nacho 0
  • nanostring 0
  • fetch 0
  • emboss 0
  • MCMICRO 0
  • antibiotics 0
  • allele-specific 0
  • norm 0
  • scatter 0
  • reheader 0
  • realignment 0
  • duplex 0
  • RiPP 0
  • standardization 0
  • NRPS 0
  • microbial 0
  • svdb 0
  • deconvolution 0
  • bayesian 0
  • purge duplications 0
  • interval list 0
  • filtermutectcalls 0
  • Duplication purging 0
  • standardise 0
  • joint genotyping 0
  • antismash 0
  • bfiles 0
  • variant pruning 0
  • otu tables 0
  • standardisation 0
  • taxonomic profile 0
  • import 0
  • panelofnormals 0
  • evidence 0
  • adapter 0
  • normalize 0
  • dereplicate 0
  • image_processing 0
  • repeats 0
  • short reads 0
  • reads merging 0
  • duplicate 0
  • ome-tif 0
  • de novo assembler 0
  • Read depth 0
  • scaffold 0
  • unaligned 0
  • contig 0
  • small genome 0
  • UMIs 0
  • merge mate pairs 0
  • rare variants 0
  • ucsc/liftover 0
  • error 0
  • eigenvectors 0
  • DNA contamination estimation 0
  • fast5 0
  • gtftogenepred 0
  • refflat 0
  • polya tail 0
  • antimicrobial peptide prediction 0
  • construct 0
  • de-novo 0
  • longread 0
  • sha256 0
  • 256 bit 0
  • decompress 0
  • fracminhash sketch 0
  • graph projection to vcf 0
  • readproteingroups 0
  • shinyngs 0
  • umicollapse 0
  • exploratory 0
  • boxplot 0
  • density 0
  • features 0
  • genepred 0
  • long read alignment 0
  • bedtobigbed 0
  • workflow_mode 0
  • eucaryotes 0
  • dnascope 0
  • dnamodelapply 0
  • readwriter 0
  • freqsum 0
  • vcfbreakmulti 0
  • denoisereadcounts 0
  • copyratios 0
  • Mycobacterium tuberculosis 0
  • uniq 0
  • deduplicate 0
  • createreadcountpanelofnormals 0
  • coding 0
  • bam2seqz 0
  • VCFtools 0
  • vcf2bed 0
  • sliding 0
  • verifybamid 0
  • bedgraphtobigwig 0
  • relative coverage 0
  • genetic sex 0
  • sex determination 0
  • hicPCA 0
  • AMPs 0
  • cds 0
  • induce 0
  • sequencing adapters 0
  • transcroder 0
  • gc_wiggle 0
  • snakemake 0
  • workflow 0
  • bigbed 0
  • scRNA-Seq 0
  • proteus 0
  • mashmap 0
  • short-read sequencing 0
  • detecting svs 0
  • upd 0
  • uniparental 0
  • disomy 0
  • maf 0
  • dbnsfp 0
  • whamg 0
  • wavefront 0
  • gemini 0
  • predictions 0
  • usearch 0
  • snv 0
  • variantcalling 0
  • sccmec 0
  • dist 0
  • streptococcus 0
  • ribosomal RNA 0
  • SNPs 0
  • spa 0
  • spatype 0
  • downsample 0
  • all versus all 0
  • invariant 0
  • downsample bam 0
  • constant 0
  • chromosomal rearrangements 0
  • pangenome-scale 0
  • subsample bam 0
  • vcf2db 0
  • wham 0
  • lua 0
  • amp 0
  • adna 0
  • sliding window 0
  • rRNA 0
  • extractunbinned 0
  • rdtest 0
  • linkbins 0
  • rdtest2vcf 0
  • countsvtypes 0
  • hash sketch 0
  • CRAM 0
  • baftest 0
  • c to t 0
  • signatures 0
  • sintax 0
  • svtk/baftest 0
  • mapad 0
  • model 0
  • sniffles 0
  • toml 0
  • snippy 0
  • core 0
  • copy-number 0
  • copy number analysis 0
  • gender determination 0
  • files 0
  • vsearch/sort 0
  • POA 0
  • SMN2 0
  • copy number alterations 0
  • copy number variation 0
  • yahs 0
  • geo 0
  • SMN1 0
  • resistance genes 0
  • groupby 0
  • staging 0
  • uniques 0
  • Illumina 0
  • functional 0
  • impute-info 0
  • tags 0
  • tag2tag 0
  • hashing-based deconvolution 0
  • rank 0
  • java 0
  • script 0
  • xml 0
  • svg 0
  • standard 0
  • haplotag 0
  • Staging 0
  • Read report 0
  • admixture 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
  • drug categorization 0
  • Read trimming 0
  • setgt 0
  • cram-size 0
  • trimfq 0
  • vcflib/vcffixup 0
  • AC/NS/AF 0
  • Pacbio 0
  • guidetree 0
  • bwamem2 0
  • bwameme 0
  • grabix 0
  • ribosomal 0
  • 10x 0
  • regulatory network 0
  • transcription factors 0
  • paraphase 0
  • selector 0
  • size 0
  • Read filters 0
  • quality check 0
  • realign 0
  • circular 0
  • spot 0
  • orthogroup 0
  • orthologs 0
  • sage 0
  • mass spectrometry 0
  • featuretable 0
  • extraction 0
  • cgMLST 0
  • WGS 0
  • redundant 0
  • nanoq 0
  • ATACshift 0
  • jvarkit 0
  • donor deconvolution 0
  • chip 0
  • scanpy 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
  • pdb 0
  • run 0
  • updatedata 0
  • partitioning 0
  • human removal 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
  • find 0
  • metagenome assembler 0
  • decontamination 0
  • translate 0
  • antimicrobial reistance 0
  • tar 0
  • tarball 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
  • adapterremoval 0
  • doublet_detection 0
  • hostile 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
  • contiguate 0
  • relabel 0
  • resegment 0
  • morphology 0
  • cellsnp 0
  • genotype-based demultiplexing 0
  • tnscope 0
  • transform 0
  • structural variant 0
  • bam2fastx 0
  • bam2fastq 0
  • immcantation 0
  • airrseq 0
  • immunoinformatics 0
  • co-orthology 0
  • homology 0
  • sequence similarity 0
  • spectral clustering 0
  • comparative genomics 0
  • deep variant 0
  • mutect 0
  • idx 0
  • gaps 0
  • rad 0
  • introns 0
  • install 0
  • joint-genotyping 0
  • genotypegvcf 0
  • affy 0
  • parallel 0
  • plastid 0
  • resfinder 0
  • pseudohaploid 0
  • raw 0
  • mgf 0
  • parquet 0
  • parser 0
  • dbsnp 0
  • Staphylococcus aureus 0
  • gost 0
  • quarto 0
  • decompose 0
  • bgen 0
  • chloroplast 0
  • confidence 0
  • blat 0
  • alr 0
  • clr 0
  • boxcox 0
  • genetic 0
  • Escherichia coli 0
  • propd 0
  • Read coverage histogram 0
  • reverse complement 0
  • simulation 0
  • hmmfetch 0
  • transmembrane 0
  • gprofiler2 0
  • genome graph 0
  • tnseq 0
  • decoy 0
  • htseq 0
  • rrna 0
  • sompy 0
  • peak picking 0
  • site frequency spectrum 0
  • ancestral alleles 0
  • derived alleles 0
  • tnfilter 0
  • array_cgh 0
  • cytosure 0
  • vector 0
  • standardize 0
  • python 0
  • lexogen 0
  • functional enrichment 0
  • structural-variants 0
  • omics 0
  • biological activity 0
  • prior knowledge 0
  • tag 0
  • cell_barcodes 0
  • mygene 0
  • go 0
  • pile up 0
  • nanopore sequencing 0
  • rna velocity 0
  • cobra 0
  • extension 0
  • grea 0
  • translation 0
  • scimap 0
  • paired reads merging 0
  • overlap-based merging 0
  • check 0
  • hamming-distance 0
  • hashing-based deconvoltion 0
  • gnu 0
  • coreutils 0
  • generic 0
  • transposable element 0
  • retrieval 0
  • MMseqs2 0
  • InterProScan 0
  • busco 0
  • droplet based single cells 0
  • Bayesian 0
  • spatial_neighborhoods 0
  • r 0
  • hwe equilibrium 0
  • coexpression 0
  • correlation 0
  • corpcor 0
  • assay 0
  • phylogenetics 0
  • minimum_evolution 0
  • distance-based 0
  • nucleotide sequence 0
  • homologs 0
  • multi-tool 0
  • predict 0
  • reference panels 0
  • hardy-weinberg 0
  • hwe statistics 0
  • reference-independent 0
  • associations 0
  • genotype likelihood 0
  • collapse 0
  • liftover 0
  • probabilistic realignment 0
  • seqfu 0
  • n50 0
  • cell_type_identification 0
  • cell_phenotyping 0
  • machine_learning 0
  • clahe 0
  • refresh 0
  • association 0
  • GWAS 0
  • case/control 0
  • pseudodiploid 0
  • gfastats 0
  • random draw 0
  • selectvariants 0
  • indexfeaturefile 0
  • csi 0
  • learnreadorientationmodel 0
  • readorientationartifacts 0
  • leftalignandtrimvariants 0
  • mergebamalignment 0
  • mutectstats 0
  • snvs 0
  • postprocessgermlinecnvcalls 0
  • preprocessintervals 0
  • printreads 0
  • printsvevidence 0
  • reblockgvcf 0
  • revert 0
  • shiftchain 0
  • getpileupsumaries 0
  • shiftfasta 0
  • shiftintervals 0
  • site depth 0
  • splitcram 0
  • splitintervals 0
  • svannotate 0
  • svcluster 0
  • variantfiltration 0
  • recalibration model 0
  • variantrecalibrator 0
  • gawk 0
  • txt 0
  • file parsing 0
  • bgc 0
  • readcountssummary 0
  • germlinevariantsites 0
  • deduping 0
  • condensedepthevidence 0
  • vqsr 0
  • asereadcounter 0
  • bedtointervallist 0
  • calculatecontamination 0
  • cross-samplecontamination 0
  • getpileupsummaries 0
  • calibratedragstrmodel 0
  • cnnscorevariants 0
  • collectreadcounts 0
  • collectsvevidence 0
  • combinegvcfs 0
  • short variant discovery 0
  • createsequencedictionary 0
  • germlinecnvcaller 0
  • createsomaticpanelofnormals 0
  • BCF 0
  • determinegermlinecontigploidy 0
  • filterintervals 0
  • filtervarianttranches 0
  • tranche filtering 0
  • gatherbqsrreports 0
  • genomicsdb 0
  • genomicsdbimport 0
  • jointgenotyping 0
  • panelofnormalscreation 0
  • germline contig ploidy 0
  • genome profile 0
  • compound 0
  • annotateintervals 0
  • mitochondrial 0
  • gunc 0
  • gunzip 0
  • yaml 0
  • gvcftools 0
  • extract_variants 0
  • extractvariants 0
  • bamtools/convert 0
  • abricate 0
  • amrfinderplus 0
  • fARGene 0
  • rgi 0
  • ibd 0
  • hbd 0
  • beagle 0
  • mouse 0
  • genome taxonomy database 0
  • Haemophilus influenzae 0
  • haplotype resolution 0
  • gccounter 0
  • readcounter 0
  • reformat 0
  • HMMER 0
  • amino acid 0
  • Hidden Markov Model 0
  • hmtnote 0
  • annotations 0
  • pos 0
  • haemophilus 0
  • panel_of_normals 0
  • IDR 0
  • archaea 0
  • bamtools/split 0
  • models 0
  • background_correction 0
  • smaller fastqs 0
  • genome size 0
  • genome heterozygosity 0
  • repeat content 0
  • Salmonella Typhi 0
  • Mykrobe 0
  • clumping fastqs 0
  • chromap 0
  • genome summary 0
  • genome manipulation 0
  • genome statistics 0
  • microscopy 0
  • gget 0
  • low coverage 0
  • illumiation_correction 0
  • GTDB taxonomy 0
  • trimBam 0
  • gstama/polyacleanup 0
  • gstama/merge 0
  • TAMA 0
  • gene model 0
  • tama_collapse.py 0
  • bamUtil 0
  • element 0
  • Sample 0
  • genomes on a tree 0
  • merge compare 0
  • GNU 0
  • joint-variant-calling 0
  • Imputation 0
  • Haplotypes 0
  • variant quality score recalibration 0
  • targets 0
  • igv.js 0
  • postprocessing 0
  • Segmentation 0
  • Cores 0
  • Assembly 0
  • custom 0
  • version 0
  • domains 0
  • na 0
  • compartments 0
  • topology 0
  • cls 0
  • calder2 0
  • gct 0
  • cutesv 0
  • cadd 0
  • pcr duplicates 0
  • UNet 0
  • paired-end 0
  • tblastn 0
  • subtyping 0
  • track 0
  • Salmonella enterica 0
  • corrrelation 0
  • scatterplot 0
  • sorted 0
  • cumulative coverage 0
  • file manipulation 0
  • bioawk 0
  • unionBedGraphs 0
  • blastx 0
  • segment 0
  • TMA dearray 0
  • mcool 0
  • duphold 0
  • crispr 0
  • duplicate removal 0
  • chromosome_visualization 0
  • splice 0
  • quality assurnce 0
  • qa 0
  • polymut 0
  • polymorphic 0
  • polymorphic sites 0
  • protein coding genes 0
  • cmseq 0
  • access 0
  • antitarget 0
  • export 0
  • target 0
  • antibody capture 0
  • genomic bins 0
  • antigen capture 0
  • partition histograms 0
  • multiomics 0
  • concoct 0
  • nucleotide composition 0
  • subcontigs 0
  • mkvdjref 0
  • cellpose 0
  • cooler/balance 0
  • cload 0
  • digest 0
  • enzyme 0
  • hifi 0
  • makebins 0
  • subtract 0
  • structural variation 0
  • heattree 0
  • random 0
  • ENA 0
  • public 0
  • closest 0
  • consensus sequence 0
  • duplexumi 0
  • groupreads 0
  • unmapped 0
  • ubam 0
  • zipperbams 0
  • bamtobed 0
  • sorting 0
  • autozygosity 0
  • single molecule 0
  • generate 0
  • homozygosity 0
  • genomecov 0
  • lint 0
  • fq 0
  • rust 0
  • variant caller 0
  • biallelic 0
  • somatic variant calling 0
  • germline variant calling 0
  • bacterial variant calling 0
  • bootstrapping 0
  • UShER 0
  • gamma 0
  • gene-calling 0
  • gangstr 0
  • update header 0
  • SRA 0
  • getfasta 0
  • depth information 0
  • split by chromosome 0
  • escherichia coli 0
  • slopBed 0
  • PEP 0
  • schema 0
  • pep 0
  • eigenstratdatabasetools 0
  • bases 0
  • sizes 0
  • eklipse 0
  • region 0
  • shiftBed 0
  • circos 0
  • deletion 0
  • multinterval 0
  • overlapped bed 0
  • ANI 0
  • chunking 0
  • ARGs 0
  • antibiotic resistance genes 0
  • faqcs 0
  • str 0
  • overlap 0
  • jaccard 0
  • maskfasta 0
  • embl 0
  • cache 0
  • percent on target 0
  • endogenous DNA 0
  • Streptococcus pyogenes 0
  • swissprot 0
  • genbank 0
  • igv 0
  • js 0
  • selection 0
  • identifiers 0
  • NETCAGE 0
  • RAMPAGE 0
  • csRNA-seq 0
  • STRIPE-seq 0
  • PRO-seq 0
  • GRO-seq 0
  • HLA 0
  • exclude 0
  • variant identifiers 0
  • subset 0
  • indep 0
  • indep pairwise 0
  • recode 0
  • whole genome association 0
  • scoring 0
  • PRO-cap 0
  • variant genetic 0
  • pmdtools 0
  • porechop_abi 0
  • contact 0
  • pretext 0
  • jpg 0
  • bmp 0
  • contact maps 0
  • gene finding 0
  • intervals coverage 0
  • genomic intervals 0
  • normal database 0
  • panel of normals 0
  • cutoff 0
  • CAGE 0
  • GRO-cap 0
  • duplicate purging 0
  • motif 0
  • pairstools 0
  • restriction fragments 0
  • select 0
  • http(s) 0
  • paragraph 0
  • graphs 0
  • pbbam 0
  • pbmerge 0
  • subreads 0
  • pbp 0
  • pair-end 0
  • read 0
  • pedigrees 0
  • utility 0
  • ChIP-Seq 0
  • CoPRO 0
  • phantom peaks 0
  • prophage 0
  • identification 0
  • illumina datasets 0
  • phylogenetic composition 0
  • hybrid-selection 0
  • mate-pair 0
  • liftovervcf 0
  • pcr 0
  • picard/renamesampleinvcf 0
  • sortvcf 0
  • deletions 0
  • insertions 0
  • tandem duplications 0
  • haplotype purging 0
  • false duplications 0
  • ligation junctions 0
  • cut&tag 0
  • calmd 0
  • faidx 0
  • insert size 0
  • repair 0
  • paired 0
  • read pairs 0
  • doCounts 0
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  • allele counts 0
  • nuclear contamination estimate 0
  • scramble 0
  • cluster analysis 0
  • clusteridentifier 0
  • peak-caller 0
  • cut&run 0
  • ampliconclip 0
  • chromatin 0
  • seacr 0
  • assembly-binning 0
  • applyvarcal 0
  • VQSR 0
  • variant recalibration 0
  • post Post-processing 0
  • subseq 0
  • grep 0
  • sequence headers 0
  • sertotype 0
  • interleave 0
  • header 0
  • seq 0
  • installation 0
  • amplicon 0
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  • fragment_size 0
  • Haplotype purging 0
  • False duplications 0
  • Assembly curation 0
  • purging 0
  • quast 0
  • neighbour-joining 0
  • subsampling 0
  • long uncorrected reads 0
  • rhocall 0
  • R 0
  • bamstat 0
  • strandedness 0
  • experiment 0
  • read_pairs 0
  • inner_distance 0
  • duplicate marking 0
  • salsa 0
  • sambamba 0
  • flagstat 0
  • multimapper 0
  • Ancestor 0
  • LCA 0
  • salsa2 0
  • rtg-tools 0
  • read distribution 0
  • rocplot 0
  • pedfilter 0
  • rtg 0
  • integrity 0
  • mapping-based 0
  • sequence-based 0
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  • genome browser 0
  • sgRNA 0
  • cycif 0
  • legionella 0
  • clinical 0
  • pneumophila 0
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  • Python 0
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  • pneumoniae 0
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  • combining 0
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  • reorder 0
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  • flip 0
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  • Beautiful stand-alone HTML report 0
  • GATK UnifiedGenotyper 0
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  • debruijn 0
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  • contour map 0
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  • pigz 0

This tool looks for low-complexity STR sequences along the reference that are later used to estimate the Dragstr model during single sample auto calibration CalibrateDragstrModel.

000

str_table versions

gatk4:

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

Estimates the numbers of unique molecules in a sequencing library.

01000

metrics versions

gatk4:

Genome Analysis Toolkit (GATK4)

A tool for quality control and tracing taxonomic origins of microRNA sequencing data

0120

html json tsv all_fa rnatype_unknown_fa versions

mirtrace:

miRTrace is a new quality control and taxonomic tracing tool developed specifically for small RNA sequencing data (sRNA-Seq). Each sample is characterized by profiling sequencing quality, read length, sequencing depth and miRNA complexity and also the amounts of miRNAs versus undesirable sequences (derived from tRNAs, rRNAs and sequencing artifacts). In addition to these routine quality control (QC) analyses, miRTrace can accurately and sensitively resolve taxonomic origins of small RNA-Seq data based on the composition of clade-specific miRNAs. This feature can be used to detect cross-clade contaminations in typical lab settings. It can also be applied for more specific applications in forensics, food quality control and clinical diagnosis, for instance tracing the origins of meat products or detecting parasitic microRNAs in host serum.

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metareadsformatmode

meta versions npa npc npl npo

Visualise metagenome redundancy curve in PNG format from a single Nonpareil npo file

01

png versions

nonpareil:

Estimate average coverage and create curves for metagenomic datasets

Calculate metagenome redundancy curve from FASTQ files

0100

npa npc npl npo versions

nonpareil:

Estimate average coverage and create curves for metagenomic datasets

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

Visualise metagenome redundancy curves in PNG format from multiple Nonpareil npo files in a single image

01

png versions

nonpareil:

Estimate average coverage and create curves for metagenomic datasets

Software for predicting library complexity and genome coverage in high-throughput sequencing

01

c_curve log versions

preseq:

Software for predicting library complexity and genome coverage in high-throughput sequencing

Software for predicting library complexity and genome coverage in high-throughput sequencing

01

lc_extrap log versions

preseq:

Software for predicting library complexity and genome coverage in high-throughput sequencing

Seqcluster collapse reduces computational complexity by collapsing identical sequences in a FASTQ file.

01

fastq versions

seqcluster:

Small RNA analysis from NGS data. Seqcluster generates a list of clusters of small RNA sequences, their genome location, their annotation and the abundance in all the sample of the project.

Masks out highly repetitive DNA sequences with low complexity in a genome

01

converted versions

windowmasker:

A program to mask highly repetitive and low complexity DNA sequences within a genome.

A program to generate frequency counts of repetitive units.

01

counts versions

windowmasker:

A program to mask highly repetitive and low complexity DNA sequences within a genome.

A program to take a counts file and creates a file of genomic co-ordinates to be masked.

0101

intervals versions

windowmasker:

A program to mask highly repetitive and low complexity DNA sequences within a genome.

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