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.

  • antimicrobial resistance 10
  • bacteria 7
  • amr 7
  • fasta 6
  • reporting 6
  • antimicrobial resistance genes 6
  • arg 5
  • antibiotic resistance 5
  • assembly 4
  • resistance 4
  • fastq 3
  • deeparg 3
  • contigs 2
  • prediction 2
  • deep learning 2
  • virulence 2
  • bam 1
  • genomics 1
  • metagenomics 1
  • database 1
  • download 1
  • illumina 1
  • serotype 1
  • normalization 1
  • typing 1
  • mlst 1
  • microbes 1
  • blastn 1
  • kma 1
  • metagenomes 1
  • identifier 1
  • metagenomic 1
  • ARGs 1
  • antibiotic resistance genes 1
  • amrfinderplus 1
  • fARGene 1
  • abricate 1
  • resfinder 1
  • resistance genes 1
  • rgi 1
  • Mycobacterium tuberculosis 1
  • antimicrobial reistance 1
  • drug categorization 1
  • mcr-1 1
  • vcf 0
  • genome 0
  • index 0
  • alignment 0
  • reference 0
  • bed 0
  • gatk4 0
  • cram 0
  • sam 0
  • sort 0
  • variant calling 0
  • structural variants 0
  • annotation 0
  • align 0
  • merge 0
  • filter 0
  • gff 0
  • map 0
  • statistics 0
  • coverage 0
  • qc 0
  • variants 0
  • quality control 0
  • gtf 0
  • classification 0
  • classify 0
  • cnv 0
  • nanopore 0
  • split 0
  • contamination 0
  • MSA 0
  • gfa 0
  • taxonomic profiling 0
  • k-mer 0
  • variant 0
  • taxonomy 0
  • sentieon 0
  • somatic 0
  • pacbio 0
  • convert 0
  • binning 0
  • quality 0
  • proteomics 0
  • count 0
  • conversion 0
  • single-cell 0
  • clustering 0
  • copy number 0
  • VCF 0
  • ancient DNA 0
  • bedtools 0
  • imputation 0
  • phylogeny 0
  • bisulfite 0
  • graph 0
  • trimming 0
  • bcftools 0
  • sv 0
  • variation graph 0
  • gvcf 0
  • isoseq 0
  • build 0
  • cna 0
  • long reads 0
  • rnaseq 0
  • wgs 0
  • bqsr 0
  • databases 0
  • mags 0
  • protein 0
  • QC 0
  • indexing 0
  • compression 0
  • bisulphite 0
  • methylseq 0
  • picard 0
  • methylation 0
  • consensus 0
  • kmer 0
  • table 0
  • imaging 0
  • metrics 0
  • long-read 0
  • phage 0
  • 5mC 0
  • mapping 0
  • visualisation 0
  • stats 0
  • demultiplex 0
  • openms 0
  • tsv 0
  • sequences 0
  • base quality score recalibration 0
  • taxonomic classification 0
  • searching 0
  • protein sequence 0
  • scWGBS 0
  • WGBS 0
  • haplotype 0
  • pairs 0
  • DNA methylation 0
  • markduplicates 0
  • bins 0
  • depth 0
  • pangenome graph 0
  • histogram 0
  • cluster 0
  • aDNA 0
  • structure 0
  • neural network 0
  • plot 0
  • matrix 0
  • expression 0
  • db 0
  • LAST 0
  • checkm 0
  • metagenome 0
  • genotype 0
  • completeness 0
  • archaeogenomics 0
  • repeat 0
  • biscuit 0
  • mmseqs2 0
  • palaeogenomics 0
  • virus 0
  • damage 0
  • bcf 0
  • mappability 0
  • filtering 0
  • annotate 0
  • validation 0
  • machine learning 0
  • transcript 0
  • bwa 0
  • cooler 0
  • low-coverage 0
  • samtools 0
  • iCLIP 0
  • bisulfite sequencing 0
  • aligner 0
  • mag 0
  • hmmsearch 0
  • gff3 0
  • decompression 0
  • segmentation 0
  • mkref 0
  • dedup 0
  • peaks 0
  • population genetics 0
  • phasing 0
  • msa 0
  • transcriptome 0
  • kraken2 0
  • glimpse 0
  • blast 0
  • bismark 0
  • example 0
  • evaluation 0
  • genotyping 0
  • complexity 0
  • seqkit 0
  • ncbi 0
  • spatial 0
  • sequence 0
  • germline 0
  • newick 0
  • umi 0
  • ucsc 0
  • gene 0
  • mirna 0
  • demultiplexing 0
  • tumor-only 0
  • differential 0
  • report 0
  • bedGraph 0
  • deduplication 0
  • vsearch 0
  • json 0
  • antimicrobial peptides 0
  • cnvkit 0
  • low frequency variant calling 0
  • prokaryote 0
  • scRNA-seq 0
  • kmers 0
  • single 0
  • pangenome 0
  • hmmer 0
  • snp 0
  • mitochondria 0
  • duplicates 0
  • NCBI 0
  • short-read 0
  • splicing 0
  • multiple sequence alignment 0
  • feature 0
  • gzip 0
  • plasmid 0
  • summary 0
  • kallisto 0
  • fragment 0
  • merging 0
  • amps 0
  • adapters 0
  • visualization 0
  • benchmark 0
  • de novo 0
  • single cell 0
  • call 0
  • mem 0
  • svtk 0
  • 3-letter genome 0
  • ptr 0
  • gridss 0
  • coptr 0
  • detection 0
  • query 0
  • deamination 0
  • de novo assembly 0
  • counts 0
  • mpileup 0
  • microbiome 0
  • extract 0
  • indels 0
  • interval 0
  • csv 0
  • sourmash 0
  • diversity 0
  • tabular 0
  • riboseq 0
  • isolates 0
  • clipping 0
  • profiling 0
  • view 0
  • MAF 0
  • text 0
  • idXML 0
  • wxs 0
  • mutect2 0
  • SV 0
  • CLIP 0
  • interval_list 0
  • haplotypecaller 0
  • cut 0
  • bin 0
  • genome assembler 0
  • circrna 0
  • bcl2fastq 0
  • bedgraph 0
  • gsea 0
  • fgbio 0
  • compare 0
  • read depth 0
  • miscoding lesions 0
  • ganon 0
  • archaeogenetics 0
  • hic 0
  • palaeogenetics 0
  • STR 0
  • phylogenetic placement 0
  • structural 0
  • profile 0
  • genmod 0
  • diamond 0
  • public datasets 0
  • bigwig 0
  • compress 0
  • peak-calling 0
  • snps 0
  • enrichment 0
  • ranking 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
  • sketch 0
  • add 0
  • ont 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
  • 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
  • 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
  • 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
  • das tool 0
  • das_tool 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
  • gene labels 0
  • polyA_tail 0
  • Read depth 0
  • repeats 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
  • 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
  • genomad 0
  • ChIP-seq 0
  • unaligned 0
  • duplex 0
  • single cells 0
  • samplesheet 0
  • regions 0
  • random forest 0
  • heatmap 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
  • 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
  • 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
  • tnscope 0
  • bgen 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
  • 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
  • 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
  • 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
  • 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
  • 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
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  • check 0
  • n50 0
  • predict 0
  • amp 0
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  • reference-independent 0
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  • seqfu 0
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  • machine_learning 0
  • embl 0
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  • split by chromosome 0
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  • refresh 0
  • association 0
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  • extraction 0
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  • Read filters 0
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  • Read report 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
  • transposable element 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
  • cancer genome 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
  • somatic structural variations 0
  • readcountssummary 0
  • mobile element insertions 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
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  • identification 0
  • amino acid 0
  • Jupyter 0
  • jupytext 0
  • papermill 0
  • tblastn 0
  • genome heterozygosity 0
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  • 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
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  • qa 0
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  • 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
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  • svcluster 0
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  • reduced 0
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  • site depth 0
  • MD5 0
  • maximum-likelihood 0
  • sgRNA 0
  • chromosome_visualization 0
  • pneumophila 0
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  • slopBed 0
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  • qualities 0
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  • illumina datasets 0
  • annotations 0
  • protein coding genes 0
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  • virulent 0
  • subseq 0
  • grep 0
  • sequence headers 0
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  • header 0
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  • seq 0
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  • random draw 0
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  • freqsum 0
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  • bam2seqz 0
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  • induce 0
  • targets 0
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  • bacphlip 0
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  • amplicon 0
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Screen assemblies for antimicrobial resistance against multiple databases

010

report versions

abricate:

Mass screening of contigs for antibiotic resistance genes

Screen assemblies for antimicrobial resistance against multiple databases

01

report versions

abricate:

Mass screening of contigs for antibiotic resistance genes

A NATA accredited tool for reporting the presence of antimicrobial resistance genes in bacterial genomes

01

matches partials virulence out txt versions

abritamr:

A pipeline for running AMRfinderPlus and collating results into functional classes

Identify antimicrobial resistance in gene or protein sequences

010

report mutation_report versions tool_version db_version

amrfinderplus:

AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences.

Identify antimicrobial resistance in gene or protein sequences

NO input

db versions

amrfinderplus:

AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences.

Normalize antibiotic resistance genes (ARGs) using the ARO ontology (developed by CARD).

0100

tsv versions

Download and prepare database for Ariba analysis

01

db versions

ariba:

ARIBA: Antibiotic Resistance Identification By Assembly

Query input FASTQs against Ariba formatted databases

0101

results versions

ariba:

ARIBA: Antibiotic Resistance Identification By Assembly

A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes

NO input

db versions

deeparg:

A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes

A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes

0120

daa daa_tsv arg potential_arg versions

deeparg:

A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes

tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.

010

log txt hmm hmm_genes orfs orfs_amino contigs contigs_pept filtered filtered_pept fragments trimmed spades metagenome tmp versions

Tool to convert and summarize ABRicate outputs using the hAMRonization specification

01000

json tsv versions

hamronization:

Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification

Tool to convert and summarize AMRfinderPlus outputs using the hAMRonization specification.

01000

json tsv versions

hamronization:

Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification

Tool to convert and summarize DeepARG outputs using the hAMRonization specification

01000

json tsv versions

hamronization:

Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification

Tool to convert and summarize fARGene outputs using the hAMRonization specification

01000

json tsv versions

hamronization:

Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification

Tool to convert and summarize RGI outputs using the hAMRonization specification.

01000

json tsv versions

hamronization:

Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification

Tool to summarize and combine all hAMRonization reports into a single file

00

json tsv html versions

hamronization:

Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification

Analysis of mcr-1 gene (mobilized colistin resistance) for sequence variation

01

tsv fa versions

AMR predictions for supported species

010

csv json versions

mykrobe:

Antibiotic resistance prediction in minutes

ResFinder identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria

01200

json disinfinder_kma pheno_table_species pheno_table pointfinder_kma pointfinder_prediction pointfinder_results pointfinder_table resfinder_hit_in_genome_seq resfinder_blast resfinder_kma resfinder_resistance_gene_seq resfinder_results_table resfinder_results_tab resfinder_results versions

resfinder:

ResFinder identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria

Preprocess the CARD database for RGI to predict antibiotic resistance from protein or nucleotide data

0

db tool_version db_version versions

rgi:

This module preprocesses the downloaded Comprehensive Antibiotic Resistance Database (CARD) which can then be used as input for RGI.

Predict antibiotic resistance from protein or nucleotide data

0100

json tsv tmp tool_version db_version versions

rgi:

This tool provides a preliminary annotation of your DNA sequence(s) based upon the data available in The Comprehensive Antibiotic Resistance Database (CARD). Hits to genes tagged with Antibiotic Resistance ontology terms will be highlighted. As CARD expands to include more pathogens, genomes, plasmids, and ontology terms this tool will grow increasingly powerful in providing first-pass detection of antibiotic resistance associated genes. See license at CARD website

Short Read Sequence Typing for Bacterial Pathogens is a program designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes.

012

gene_results fullgene_results mlst_results pileup sorted_bam versions

srst2:

Short Read Sequence Typing for Bacterial Pathogens

A tool to detect resistance and lineages of M. tuberculosis genomes

01

bam csv json txt vcf versions

tbprofiler:

Profiling tool for Mycobacterium tuberculosis to detect drug resistance and lineage from WGS data

Click here to trigger an update.