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.

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

Estimate the post-mortem damage patterns of DNA

012300

empiric exponential counts table versions

atlas:

ATLAS, a suite of methods to accurately genotype and estimate genetic diversity

Gives an estimation of the sequencing bias based on known invariant sites

0123400

recal_patterns versions

atlas:

ATLAS, a suite of methods to accurately genotype and estimate genetic diversity

Use deamination patterns to estimate contamination in single-stranded libraries

010101

txt versions

authentict:

Estimates present-day DNA contamination in ancient DNA single-stranded libraries.

A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage

01000

results versions

If you are like many computer users, you would frequently like to make changes in various text files wherever certain patterns appear, or extract data from parts of certain lines while discarding the rest. The job is easy with awk, especially the GNU implementation gawk.

010

output versions

Haplocheck detects contamination patterns in mtDNA AND WGS sequencing studies by analyzing the mitochondrial DNA. Haplocheck also works as a proxy tool for nDNA studies and provides users a graphical report to investigate the contamination further. Internally, it uses the Haplogrep tool, that supports rCRS and RSRS mitochondrial versions.

01

txt html versions

Computational framework for tracking and quantifying DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.

010

runtime_log fragmisincorporation_plot length_plot misincorporation lgdistribution dnacomp stats_out_mcmc_hist stats_out_mcmc_iter stats_out_mcmc_trace stats_out_mcmc_iter_summ_stat stats_out_mcmc_post_pred stats_out_mcmc_correct_prob dnacomp_genome rescaled pctot_freq pgtoa_freq fasta folder versions

pmdtools command to filter ancient DNA molecules from others

01200

bam versions

pmdtools:

Compute postmortem damage patterns and decontaminate ancient genomes

ripgrep recursively searches directories for a regex pattern

0100

txt versions

pigz:

Parallel implementation of the gzip algorithm.

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