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.

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

Use k-mers to rapidly subtype S. enterica genomes

010

summary kmer_results simple_summary versions

Genotype Salmonella Typhi from Mykrobe results

01

tsv versions

genotyphi:

Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)

Salmonella serotype prediction from reads and assemblies

01

log tsv txt versions

Serovar prediction of salmonella assemblies

01

tsv allele_fasta allele_json cgmlst_csv versions

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