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
  • long reads 1
  • demultiplex 1
  • repeat 1
  • annotate 1
  • scRNA-seq 1
  • transposons 1
  • repeats 1
  • element 1
  • transposable element 1
  • cancer genome 1
  • somatic structural variations 1
  • mobile element insertions 1
  • svannotate 1
  • bam 0
  • genome 0
  • index 0
  • alignment 0
  • reference 0
  • assembly 0
  • bed 0
  • cram 0
  • sort 0
  • sam 0
  • variant calling 0
  • annotation 0
  • align 0
  • merge 0
  • filter 0
  • gff 0
  • bacteria 0
  • map 0
  • statistics 0
  • coverage 0
  • qc 0
  • variants 0
  • classification 0
  • classify 0
  • quality control 0
  • gtf 0
  • cnv 0
  • split 0
  • MSA 0
  • k-mer 0
  • contamination 0
  • variant 0
  • taxonomy 0
  • taxonomic profiling 0
  • gfa 0
  • sentieon 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
  • 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
  • rnaseq 0
  • databases 0
  • cna 0
  • consensus 0
  • bisulphite 0
  • QC 0
  • methylseq 0
  • protein 0
  • methylation 0
  • compression 0
  • stats 0
  • visualisation 0
  • serotype 0
  • openms 0
  • metrics 0
  • tsv 0
  • imaging 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
  • mmseqs2 0
  • mappability 0
  • db 0
  • samtools 0
  • machine learning 0
  • iCLIP 0
  • checkm 0
  • genotype 0
  • bwa 0
  • damage 0
  • completeness 0
  • metagenome 0
  • filtering 0
  • LAST 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
  • complexity 0
  • example 0
  • phasing 0
  • genotyping 0
  • ucsc 0
  • sequence 0
  • transcriptome 0
  • kraken2 0
  • dedup 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
  • antimicrobial peptides 0
  • pangenome 0
  • splicing 0
  • json 0
  • multiple sequence alignment 0
  • cnvkit 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
  • diversity 0
  • tabular 0
  • single cell 0
  • text 0
  • sourmash 0
  • call 0
  • FASTQ 0
  • fragment 0
  • csv 0
  • cat 0
  • mem 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
  • MAF 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
  • redundancy 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
  • 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
  • duplication 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
  • 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
  • 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
  • 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
  • multiqc 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
  • seqfu 0
  • n50 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
  • 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
  • spliced 0
  • train 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
  • bioinformatics tools 0
  • Beautiful stand-alone HTML report 0
  • GATK UnifiedGenotyper 0
  • SNP table 0
  • contaminant 0
  • public 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
  • 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

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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