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.

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

Demultiplex Element Biosciences bases files

012

sample_fastq sample_json qc_report run_stats generated_run_manifest metrics unassigned versions

Adds predicted functional consequence, gene overlap, and noncoding element overlap annotations to SV VCF from GATK-SV pipeline. Input files are an SV VCF, a GTF file containing primary or canonical transcripts, and a BED file containing noncoding elements. Output file is an annotated SV VCF.

0123000

annotated_vcf index versions

gatk4:

Genome Analysis Toolkit (GATK4)

Download geNomad databases and related files

NO input

genomad_db versions

genomad:

Identification of mobile genetic elements

Identify mobile genetic elements present in genomic assemblies

010

aggregated_classification taxonomy provirus compositions calibrated_classification plasmid_fasta plasmid_genes plasmid_proteins plasmid_summary virus_fasta virus_genes virus_proteins virus_summary versions

genomad:

Identification of mobile genetic elements

Quantification of transposable elements expression in scRNA-seq

0100

versions results counts log tmp

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

012

insertions insertions_index deletions deletions_index rearrangements rearrangements_index bp_info bp_info_index versions

nanomonsv:

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

Performs de novo transposable element (TE) family identification with RepeatModeler

01

fasta stk log versions

repeatmodeler:

RepeatModeler is a de-novo repeat family identification and modeling package.

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