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.

  • reporting 7
  • vcf 6
  • assembly 6
  • structural variants 6
  • antimicrobial resistance 6
  • amr 6
  • genome 5
  • vsearch 5
  • detection 5
  • gridss 5
  • fasta 4
  • genomics 4
  • metagenomics 4
  • bam 3
  • index 3
  • bacteria 3
  • quality control 3
  • isoseq 3
  • antimicrobial resistance genes 3
  • prokaryote 3
  • arg 3
  • ont 3
  • fcs-gx 3
  • chimeras 3
  • long_read 3
  • minimap2 3
  • uLTRA 3
  • arriba 3
  • fusion 3
  • alignment 2
  • bed 2
  • database 2
  • align 2
  • download 2
  • contamination 2
  • copy number 2
  • neural network 2
  • population genetics 2
  • cnvkit 2
  • splicing 2
  • riboseq 2
  • circrna 2
  • deep learning 2
  • fungi 2
  • BGC 2
  • biosynthetic gene cluster 2
  • microsatellite 2
  • bedpe 2
  • somatic variants 2
  • amplicon sequences 2
  • genomes 2
  • msisensor-pro 2
  • micro-satellite-scan 2
  • tumor 2
  • msi 2
  • mirdeep2 2
  • RNA sequencing 2
  • cleaning 2
  • screening 2
  • orf 2
  • fusions 2
  • RNA-Seq 2
  • random forest 2
  • reference 1
  • cram 1
  • sort 1
  • variant calling 1
  • somatic 1
  • taxonomy 1
  • proteomics 1
  • single-cell 1
  • clustering 1
  • contigs 1
  • sv 1
  • openms 1
  • imaging 1
  • checkm 1
  • hmmsearch 1
  • spatial 1
  • ncbi 1
  • antimicrobial peptides 1
  • mitochondria 1
  • amps 1
  • summary 1
  • antibiotic resistance 1
  • microbiome 1
  • profile 1
  • SV 1
  • ampir 1
  • parsing 1
  • mzml 1
  • mtDNA 1
  • mapper 1
  • miRNA 1
  • cfDNA 1
  • polishing 1
  • amplify 1
  • deeparg 1
  • neubi 1
  • DRAMP 1
  • macrel 1
  • instability 1
  • instrain 1
  • doublets 1
  • amptransformer 1
  • ampgram 1
  • fetch 1
  • peak picking 1
  • amrfinderplus 1
  • fARGene 1
  • abricate 1
  • rgi 1
  • sintax 1
  • vsearch/sort 1
  • usearch 1
  • vsearch/fastqfilter 1
  • fastqfilter 1
  • doublet_detection 1
  • deletion 1
  • circos 1
  • eklipse 1
  • gunc 1
  • spot 1
  • MMseqs2 1
  • InterProScan 1
  • microsatellite instability 1
  • scan 1
  • population genomics 1
  • bgc 1
  • fastq 0
  • gatk4 0
  • sam 0
  • annotation 0
  • merge 0
  • filter 0
  • gff 0
  • map 0
  • statistics 0
  • coverage 0
  • qc 0
  • variants 0
  • gtf 0
  • classify 0
  • cnv 0
  • nanopore 0
  • split 0
  • MSA 0
  • gfa 0
  • k-mer 0
  • variant 0
  • classification 0
  • taxonomic profiling 0
  • pacbio 0
  • sentieon 0
  • convert 0
  • quality 0
  • count 0
  • binning 0
  • conversion 0
  • ancient DNA 0
  • VCF 0
  • imputation 0
  • bedtools 0
  • phylogeny 0
  • graph 0
  • gvcf 0
  • bcftools 0
  • variation graph 0
  • bisulfite 0
  • build 0
  • trimming 0
  • cna 0
  • bisulphite 0
  • methylseq 0
  • methylation 0
  • compression 0
  • rnaseq 0
  • databases 0
  • protein 0
  • illumina 0
  • table 0
  • wgs 0
  • kmer 0
  • indexing 0
  • picard 0
  • consensus 0
  • QC 0
  • bqsr 0
  • demultiplex 0
  • visualisation 0
  • long-read 0
  • phage 0
  • tsv 0
  • 5mC 0
  • mapping 0
  • stats 0
  • metrics 0
  • serotype 0
  • sequences 0
  • searching 0
  • protein sequence 0
  • DNA methylation 0
  • pairs 0
  • haplotype 0
  • scWGBS 0
  • histogram 0
  • pangenome graph 0
  • WGBS 0
  • markduplicates 0
  • base quality score recalibration 0
  • bins 0
  • depth 0
  • cluster 0
  • aDNA 0
  • structure 0
  • plot 0
  • matrix 0
  • expression 0
  • mags 0
  • LAST 0
  • metagenome 0
  • completeness 0
  • genotype 0
  • iCLIP 0
  • repeat 0
  • mmseqs2 0
  • annotate 0
  • palaeogenomics 0
  • virus 0
  • archaeogenomics 0
  • bcf 0
  • mappability 0
  • damage 0
  • filtering 0
  • db 0
  • machine learning 0
  • validation 0
  • aligner 0
  • long reads 0
  • bwa 0
  • biscuit 0
  • samtools 0
  • low-coverage 0
  • cooler 0
  • transcript 0
  • bisulfite sequencing 0
  • mag 0
  • gene 0
  • gff3 0
  • decompression 0
  • segmentation 0
  • mkref 0
  • dedup 0
  • peaks 0
  • transcriptome 0
  • msa 0
  • kraken2 0
  • glimpse 0
  • example 0
  • blast 0
  • evaluation 0
  • bismark 0
  • genotyping 0
  • phasing 0
  • umi 0
  • germline 0
  • ucsc 0
  • newick 0
  • sequence 0
  • complexity 0
  • seqkit 0
  • differential 0
  • tumor-only 0
  • report 0
  • demultiplexing 0
  • bedGraph 0
  • prediction 0
  • mirna 0
  • json 0
  • deduplication 0
  • low frequency variant calling 0
  • scRNA-seq 0
  • kmers 0
  • pangenome 0
  • plasmid 0
  • short-read 0
  • gzip 0
  • NCBI 0
  • taxonomic classification 0
  • hmmer 0
  • duplicates 0
  • multiple sequence alignment 0
  • feature 0
  • single 0
  • snp 0
  • 3-letter genome 0
  • ptr 0
  • deamination 0
  • kallisto 0
  • adapters 0
  • merging 0
  • benchmark 0
  • svtk 0
  • de novo 0
  • mem 0
  • single cell 0
  • coptr 0
  • fragment 0
  • call 0
  • query 0
  • visualization 0
  • isolates 0
  • mutect2 0
  • view 0
  • idXML 0
  • interval 0
  • indels 0
  • mpileup 0
  • counts 0
  • extract 0
  • csv 0
  • diversity 0
  • tabular 0
  • sourmash 0
  • clipping 0
  • text 0
  • wxs 0
  • de novo assembly 0
  • MAF 0
  • profiling 0
  • miscoding lesions 0
  • haplotypecaller 0
  • fgbio 0
  • CLIP 0
  • ganon 0
  • bcl2fastq 0
  • gsea 0
  • archaeogenetics 0
  • STR 0
  • bin 0
  • snps 0
  • interval_list 0
  • cut 0
  • hic 0
  • bedgraph 0
  • genome assembler 0
  • palaeogenetics 0
  • diamond 0
  • bigwig 0
  • structural 0
  • compress 0
  • peak-calling 0
  • public datasets 0
  • compare 0
  • phylogenetic placement 0
  • enrichment 0
  • read depth 0
  • ranking 0
  • genmod 0
  • 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
  • resistance 0
  • union 0
  • xeniumranger 0
  • ancestry 0
  • pypgx 0
  • isomir 0
  • microarray 0
  • retrotransposon 0
  • malt 0
  • telomere 0
  • redundancy 0
  • propr 0
  • logratio 0
  • family 0
  • bgzip 0
  • ccs 0
  • hmmcopy 0
  • DNA sequence 0
  • reference-free 0
  • reads 0
  • quantification 0
  • ngscheckmate 0
  • containment 0
  • matching 0
  • HiFi 0
  • preprocessing 0
  • happy 0
  • reports 0
  • notebook 0
  • gatk4spark 0
  • ligate 0
  • windowmasker 0
  • pseudoalignment 0
  • krona chart 0
  • npz 0
  • variant_calling 0
  • typing 0
  • entrez 0
  • guide tree 0
  • covid 0
  • organelle 0
  • transcriptomics 0
  • repeat expansion 0
  • PacBio 0
  • fingerprint 0
  • PCA 0
  • ambient RNA removal 0
  • HMM 0
  • amplicon sequencing 0
  • rna_structure 0
  • RNA 0
  • genotype-based deconvoltion 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
  • 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
  • panel 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
  • RNA-seq 0
  • eukaryotes 0
  • prokaryotes 0
  • cut up 0
  • cool 0
  • genome mining 0
  • angsd 0
  • remove 0
  • roh 0
  • CRISPR 0
  • bracken 0
  • mkfastq 0
  • image 0
  • nucleotide 0
  • hi-c 0
  • kraken 0
  • microbes 0
  • bwameth 0
  • aln 0
  • abundance 0
  • checkv 0
  • rna 0
  • atac-seq 0
  • chip-seq 0
  • combine 0
  • comparisons 0
  • chromosome 0
  • fai 0
  • intervals 0
  • converter 0
  • wig 0
  • png 0
  • dump 0
  • highly_multiplexed_imaging 0
  • C to T 0
  • virulence 0
  • das tool 0
  • das_tool 0
  • prefetch 0
  • removal 0
  • gwas 0
  • nextclade 0
  • Pharmacogenetics 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
  • reheader 0
  • concat 0
  • read-group 0
  • tbi 0
  • ped 0
  • intersect 0
  • GPU-accelerated 0
  • normalize 0
  • norm 0
  • scatter 0
  • windows 0
  • megan 0
  • minhash 0
  • checksum 0
  • hlala_typing 0
  • proteome 0
  • ichorcna 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
  • krakenuniq 0
  • krakentools 0
  • screen 0
  • khmer 0
  • bustools 0
  • awk 0
  • anndata 0
  • BAM 0
  • blastn 0
  • gene labels 0
  • polyA_tail 0
  • Read depth 0
  • 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
  • salmon 0
  • kma 0
  • long terminal retrotransposon 0
  • long terminal repeat 0
  • retrotransposons 0
  • MaltExtract 0
  • function 0
  • pharokka 0
  • bloom filter 0
  • orthology 0
  • k-mer index 0
  • COBS 0
  • archive 0
  • xz 0
  • authentication 0
  • genetics 0
  • edit distance 0
  • mudskipper 0
  • transcriptomic 0
  • parallelized 0
  • vcflib 0
  • distance 0
  • polish 0
  • xenograft 0
  • Streptococcus pneumoniae 0
  • sequenzautils 0
  • transformation 0
  • rename 0
  • seqtk 0
  • salmonella 0
  • varcal 0
  • 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
  • simulate 0
  • artic 0
  • aggregate 0
  • demultiplexed reads 0
  • variation 0
  • taxon tables 0
  • otu tables 0
  • standardisation 0
  • standardise 0
  • standardization 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
  • 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
  • heatmap 0
  • metagenomes 0
  • structural-variant calling 0
  • rna-seq 0
  • deseq2 0
  • blastp 0
  • fasterq-dump 0
  • eido 0
  • format 0
  • validate 0
  • eigenstrat 0
  • sra-tools 0
  • settings 0
  • emboss 0
  • correction 0
  • tab 0
  • metadata 0
  • repeat_expansions 0
  • expansionhunterdenovo 0
  • identifier 0
  • metagenomic 0
  • GEO 0
  • genome bins 0
  • microbial 0
  • concordance 0
  • phase 0
  • vdj 0
  • hmtnote 0
  • ancestral alleles 0
  • hifi 0
  • htseq 0
  • rrna 0
  • installation 0
  • sompy 0
  • doCounts 0
  • extractvariants 0
  • allele counts 0
  • site frequency spectrum 0
  • derived alleles 0
  • ANI 0
  • tnfilter 0
  • nuclear contamination estimate 0
  • ARGs 0
  • antibiotic resistance genes 0
  • faqcs 0
  • array_cgh 0
  • cytosure 0
  • post Post-processing 0
  • vector 0
  • gprofiler2 0
  • gost 0
  • str 0
  • decoy 0
  • genome graph 0
  • tnseq 0
  • 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
  • resfinder 0
  • resistance genes 0
  • raw 0
  • mgf 0
  • parquet 0
  • dbsnp 0
  • model 0
  • standardize 0
  • swissprot 0
  • quarto 0
  • python 0
  • r 0
  • coexpression 0
  • correlation 0
  • corpcor 0
  • assay 0
  • phylogenetics 0
  • minimum_evolution 0
  • distance-based 0
  • percent on target 0
  • cache 0
  • mcool 0
  • structural variant 0
  • bam2fastx 0
  • bam2fastq 0
  • immcantation 0
  • airrseq 0
  • immunoinformatics 0
  • co-orthology 0
  • homology 0
  • sequence similarity 0
  • spectral clustering 0
  • comparative genomics 0
  • genomic bins 0
  • deep variant 0
  • genotypegvcf 0
  • mutect 0
  • idx 0
  • UNet 0
  • TMA dearray 0
  • Segmentation 0
  • transform 0
  • gaps 0
  • introns 0
  • Cores 0
  • Sample 0
  • install 0
  • joint-genotyping 0
  • groupby 0
  • ibd 0
  • consensus sequence 0
  • single molecule 0
  • refflat 0
  • gtftogenepred 0
  • ucsc/liftover 0
  • mkarv 0
  • fq 0
  • lint 0
  • partition histograms 0
  • umicollapse 0
  • random 0
  • scRNA-Seq 0
  • generate 0
  • files 0
  • bedtobigbed 0
  • haplogroups 0
  • mitochondrial 0
  • beagle 0
  • upd 0
  • uniparental 0
  • disomy 0
  • snv 0
  • downsample 0
  • downsample bam 0
  • subsample bam 0
  • vcf2db 0
  • gemini 0
  • genepred 0
  • bigbed 0
  • lua 0
  • polya tail 0
  • short-read sequencing 0
  • germline variant calling 0
  • sequencing_bias 0
  • svtk/baftest 0
  • baftest 0
  • countsvtypes 0
  • rdtest2vcf 0
  • rdtest 0
  • somatic variant calling 0
  • vcf2bed 0
  • decompress 0
  • post mortem damage 0
  • fast5 0
  • bedgraphtobigwig 0
  • target 0
  • variant caller 0
  • rust 0
  • Assembly 0
  • Mycobacterium tuberculosis 0
  • chromosomal rearrangements 0
  • eucaryotes 0
  • coding 0
  • cds 0
  • transcroder 0
  • sequencing adapters 0
  • atlas 0
  • maf 0
  • toml 0
  • homologs 0
  • eigenvectors 0
  • copy number alterations 0
  • copy number variation 0
  • yahs 0
  • geo 0
  • mapad 0
  • adna 0
  • c to t 0
  • unmapped 0
  • proteus 0
  • readproteingroups 0
  • groupreads 0
  • hicPCA 0
  • gender determination 0
  • sliding 0
  • subcontigs 0
  • snakemake 0
  • workflow 0
  • workflow_mode 0
  • duplexumi 0
  • createreadcountpanelofnormals 0
  • copyratios 0
  • denoisereadcounts 0
  • readwriter 0
  • dnamodelapply 0
  • dnascope 0
  • ubam 0
  • copy number analysis 0
  • hbd 0
  • linkbins 0
  • vcfbreakmulti 0
  • uniq 0
  • deduplicate 0
  • VCFtools 0
  • verifybamid 0
  • DNA contamination estimation 0
  • concoct 0
  • construct 0
  • graph projection to vcf 0
  • nucleotide composition 0
  • http(s) 0
  • extractunbinned 0
  • utility 0
  • copy-number 0
  • zipperbams 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
  • 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
  • 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
  • relabel 0
  • barcodes 0
  • pcr duplicates 0
  • subsetting 0
  • logFC 0
  • significance statistic 0
  • p-value 0
  • scvi 0
  • solo 0
  • import segmentation 0
  • nuclear segmentation 0
  • cell segmentation 0
  • adapterremoval 0
  • paired-end 0
  • plotting 0
  • resegment 0
  • morphology 0
  • antimicrobial reistance 0
  • hostile 0
  • decontamination 0
  • human removal 0
  • metagenome assembler 0
  • cumulative coverage 0
  • mkvdjref 0
  • scanpy 0
  • contiguate 0
  • scatterplot 0
  • tag2tag 0
  • impute-info 0
  • multi-tool 0
  • na 0
  • omics 0
  • biological activity 0
  • prior knowledge 0
  • tag 0
  • cell_barcodes 0
  • mygene 0
  • go 0
  • version 0
  • pile up 0
  • Bayesian 0
  • cellpose 0
  • archaea 0
  • eigenstratdatabasetools 0
  • nanopore sequencing 0
  • rna velocity 0
  • cobra 0
  • extension 0
  • grea 0
  • genome taxonomy database 0
  • functional enrichment 0
  • translation 0
  • paired reads merging 0
  • structural-variants 0
  • scimap 0
  • check 0
  • n50 0
  • predict 0
  • amp 0
  • genbank 0
  • hardy-weinberg 0
  • hwe statistics 0
  • hwe equilibrium 0
  • reference-independent 0
  • genotype likelihood 0
  • collapse 0
  • liftover 0
  • probabilistic realignment 0
  • seqfu 0
  • cell_type_identification 0
  • spatial_neighborhoods 0
  • cell_phenotyping 0
  • machine_learning 0
  • embl 0
  • split by chromosome 0
  • clahe 0
  • refresh 0
  • association 0
  • GWAS 0
  • case/control 0
  • custom 0
  • associations 0
  • overlap-based merging 0
  • pep 0
  • functional 0
  • mass spectrometry 0
  • transcription factors 0
  • paraphase 0
  • selector 0
  • cram-size 0
  • size 0
  • quality check 0
  • realign 0
  • circular 0
  • orthogroup 0
  • orthologs 0
  • sage 0
  • featuretable 0
  • regulatory network 0
  • extraction 0
  • cgMLST 0
  • WGS 0
  • redundant 0
  • nanoq 0
  • Read filters 0
  • Read trimming 0
  • Read report 0
  • drug categorization 0
  • Imputation 0
  • uniques 0
  • Illumina 0
  • PEP 0
  • gstama/polyacleanup 0
  • hamming-distance 0
  • lexogen 0
  • hashing-based deconvoltion 0
  • gnu 0
  • coreutils 0
  • generic 0
  • transposable element 0
  • retrieval 0
  • schema 0
  • Haplotypes 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
  • mitochondrial genome 0
  • mergebamalignment 0
  • leftalignandtrimvariants 0
  • readorientationartifacts 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
  • reformat 0
  • identification 0
  • amino acid 0
  • Jupyter 0
  • jupytext 0
  • papermill 0
  • tblastn 0
  • genome heterozygosity 0
  • genome size 0
  • subtyping 0
  • Salmonella enterica 0
  • kallisto/index 0
  • quant 0
  • sorted 0
  • chromap 0
  • jasmine 0
  • digital normalization 0
  • models 0
  • k-mer counting 0
  • effective genome size 0
  • compound 0
  • Klebsiella 0
  • pneumoniae 0
  • file manipulation 0
  • kegg 0
  • kofamscan 0
  • genome profile 0
  • combining 0
  • Python 0
  • jasminesv 0
  • HMMER 0
  • pixel classification 0
  • genome summary 0
  • pos 0
  • haemophilus 0
  • Hidden Markov Model 0
  • gfastats 0
  • panel_of_normals 0
  • IDR 0
  • igv 0
  • igv.js 0
  • js 0
  • genome browser 0
  • multicut 0
  • pixel_classification 0
  • repeat content 0
  • probability_maps 0
  • genome manipulation 0
  • postprocessing 0
  • interproscan 0
  • qa 0
  • genome statistics 0
  • genomic islands 0
  • insertion 0
  • quality assurnce 0
  • Mykrobe 0
  • Salmonella Typhi 0
  • bioawk 0
  • duplicate removal 0
  • 128 bit 0
  • mash/sketch 0
  • rra 0
  • sizes 0
  • region 0
  • shiftBed 0
  • DNA damage 0
  • NGS 0
  • damage patterns 0
  • multinterval 0
  • estimate 0
  • overlapped bed 0
  • taxonomic assignment 0
  • svcluster 0
  • svannotate 0
  • CRISPR-Cas9 0
  • reduced 0
  • representations 0
  • splitintervals 0
  • maxbin2 0
  • maskfasta 0
  • metagenome-assembled genomes 0
  • chunking 0
  • mass-spectroscopy 0
  • splitcram 0
  • mcr-1 0
  • site depth 0
  • MD5 0
  • maximum-likelihood 0
  • sgRNA 0
  • chromosome_visualization 0
  • pneumophila 0
  • unionBedGraphs 0
  • file parsing 0
  • subtract 0
  • reorder 0
  • spliced 0
  • train 0
  • adapter removal 0
  • collapsing 0
  • txt 0
  • legionella 0
  • clinical 0
  • gawk 0
  • functional genomics 0
  • variantrecalibrator 0
  • limma 0
  • Listeria monocytogenes 0
  • recalibration model 0
  • slopBed 0
  • variantfiltration 0
  • lofreq/call 0
  • lofreq/filter 0
  • qualities 0
  • AMP 0
  • peptide prediction 0
  • bases 0
  • prophage 0
  • illumina datasets 0
  • annotations 0
  • protein coding genes 0
  • VQSR 0
  • variant recalibration 0
  • virulent 0
  • subseq 0
  • grep 0
  • sequence headers 0
  • polymorphic sites 0
  • sertotype 0
  • topology 0
  • interleave 0
  • temperate 0
  • header 0
  • applyvarcal 0
  • seq 0
  • cmseq 0
  • selection 0
  • random draw 0
  • pseudohaploid 0
  • pseudodiploid 0
  • freqsum 0
  • annotateintervals 0
  • bam2seqz 0
  • gc_wiggle 0
  • induce 0
  • targets 0
  • variant quality score recalibration 0
  • bacphlip 0
  • genetic sex 0
  • antibody capture 0
  • amplicon 0
  • ampliconclip 0
  • calibratedragstrmodel 0
  • calmd 0
  • getpileupsummaries 0
  • cross-samplecontamination 0
  • faidx 0
  • calculatecontamination 0
  • insert size 0
  • repair 0
  • paired 0
  • read pairs 0
  • readgroup 0
  • assembly-binning 0
  • bedtointervallist 0
  • asereadcounter 0
  • antigen capture 0
  • scramble 0
  • cluster analysis 0
  • clusteridentifier 0
  • peak-caller 0
  • cut&tag 0
  • cut&run 0
  • chromatin 0
  • seacr 0
  • vqsr 0
  • sex determination 0
  • relative coverage 0
  • sambamba 0
  • ribosomal RNA 0
  • UShER 0
  • dbnsfp 0
  • predictions 0
  • bootstrapping 0
  • SNPs 0
  • invariant 0
  • constant 0
  • cycif 0
  • background 0
  • single-stranded 0
  • ancientDNA 0
  • rRNA 0
  • export 0
  • gene-calling 0
  • authentict 0
  • haplotype resolution 0
  • signatures 0
  • hash sketch 0
  • fracminhash sketch 0
  • read group 0
  • Haemophilus influenzae 0
  • bacterial variant calling 0
  • spatype 0
  • spa 0
  • streptococcus 0
  • sccmec 0
  • gamma 0
  • multiomics 0
  • compartments 0
  • boxplot 0
  • lifestyle 0
  • domains 0
  • rare variants 0
  • error 0
  • heattree 0
  • de-novo 0
  • longread 0
  • sha256 0
  • 256 bit 0
  • access 0
  • shinyngs 0
  • exploratory 0
  • density 0
  • dist 0
  • features 0
  • antitarget 0
  • sliding window 0
  • gangstr 0
  • autofluorescence 0
  • CRAM 0
  • SMN1 0
  • SMN2 0
  • POA 0
  • sniffles 0
  • core 0
  • snippy 0
  • duplicate marking 0
  • flagstat 0
  • phylogenetic composition 0
  • variant genetic 0
  • subset 0
  • splice 0
  • indep 0
  • gget 0
  • indep pairwise 0
  • recode 0
  • whole genome association 0
  • filterintervals 0
  • identifiers 0
  • scoring 0
  • estimatelibrarycomplexity 0
  • pmdtools 0
  • variant identifiers 0
  • porechop_abi 0
  • duplication metrics 0
  • microscopy 0
  • determinegermlinecontigploidy 0
  • gccounter 0
  • background_correction 0
  • contact 0
  • pretext 0
  • jpg 0
  • bmp 0
  • contact maps 0
  • gene finding 0
  • filtervarianttranches 0
  • exclude 0
  • element 0
  • tandem duplications 0
  • csi 0
  • genomicsdb 0
  • gatherbqsrreports 0
  • tranche filtering 0
  • hybrid-selection 0
  • mate-pair 0
  • liftovervcf 0
  • pcr 0
  • picard/renamesampleinvcf 0
  • sortvcf 0
  • deletions 0
  • insertions 0
  • CoPRO 0
  • clumping fastqs 0
  • GRO-cap 0
  • PRO-cap 0
  • CAGE 0
  • NETCAGE 0
  • RAMPAGE 0
  • csRNA-seq 0
  • STRIPE-seq 0
  • PRO-seq 0
  • GRO-seq 0
  • genetic 0
  • deduping 0
  • smaller fastqs 0
  • illumiation_correction 0
  • intervals coverage 0
  • multimapper 0
  • mapping-based 0
  • short variant discovery 0
  • bamstat 0
  • bamtools/convert 0
  • strandedness 0
  • experiment 0
  • read_pairs 0
  • fragment_size 0
  • inner_distance 0
  • combinegvcfs 0
  • read distribution 0
  • polymorphic 0
  • sequence-based 0
  • mouse 0
  • composestrtablefile 0
  • integrity 0
  • rtg 0
  • collectsvevidence 0
  • pedfilter 0
  • rocplot 0
  • collectreadcounts 0
  • rtg-tools 0
  • cnnscorevariants 0
  • salsa 0
  • salsa2 0
  • LCA 0
  • Ancestor 0
  • R 0
  • rhocall 0
  • trimBam 0
  • polymut 0
  • bamUtil 0
  • calder2 0
  • genomic intervals 0
  • normal database 0
  • panel of normals 0
  • cutoff 0
  • createsomaticpanelofnormals 0
  • haplotype purging 0
  • duplicate purging 0
  • false duplications 0
  • assembly curation 0
  • Haplotype purging 0
  • False duplications 0
  • long uncorrected reads 0
  • Assembly curation 0
  • createsequencedictionary 0
  • track 0
  • purging 0
  • bamtools/split 0
  • yaml 0
  • quast 0
  • low coverage 0
  • condensedepthevidence 0
  • dragstr 0
  • neighbour-joining 0
  • subsampling 0
  • mzML 0

A submodule that parses and standardizes the results from various antimicrobial peptide identification tools.

0100000

sample_dir contig_gbks db_tsv tsv faa sample_log full_log db db_txt db_fasta db_mmseqs versions

ampcombi2/parsetables:

A parsing tool to convert and summarise the outputs from multiple AMP detection tools in a standardized format.

Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data.

metabammeta2fastameta3gtfmeta4blacklistmeta5known_fusionsmeta6structural_variantsmeta7tagsmeta8protein_domains

meta versions fusions fusions_fail

Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data.

0101010000

fusions fusions_fail versions

arriba:

Fast and accurate gene fusion detection from RNA-Seq data

Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data.

0

blacklist cytobands protein_domains known_fusions versions

arriba:

Fast and accurate gene fusion detection from RNA-Seq data

Copy number variant detection from high-throughput sequencing data

012010101010

bed cnn cnr cns pdf png versions

cnvkit:

CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.

Copy number variant detection from high-throughput sequencing data

012

tsv cnn versions

cnvkit:

CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.

Database download module for DeepBGC which detects BGCs in bacterial and fungal genomes using deep learning.

NO input

db versions

deepbgc:

DeepBGC - Biosynthetic Gene Cluster detection and classification

DeepBGC detects BGCs in bacterial and fungal genomes using deep learning.

010

readme log json bgc_gbk bgc_tsv full_gbk pfam_tsv bgc_png pr_png roc_png score_png versions

deepbgc:

DeepBGC - Biosynthetic Gene Cluster detection and classification

Doublet detection in single-cell RNA-seq data

01

h5ad predictions versions

Dysgu calls structural variants (SVs) from mapped sequencing reads. It is designed for accurate and efficient detection of structural variations.

012012

vcf tbi versions

tool for detection and quantification of large mtDNA rearrangements.

0120

deletions genes circos versions

Runs FCS-GX (Foreign Contamination Screen - Genome eXtractor) to remove foreign contamination from genome assemblies

012

cleaned contaminants versions

fcsgx:

The NCBI Foreign Contamination Screen. Genomic cross-species aligner, for contamination detection.

Fetches the NCBI FCS-GX database using a provided manifest URL

0

database versions

fcsgx:

The NCBI Foreign Contamination Screen. Genomic cross-species aligner, for contamination detection.

Runs FCS-GX (Foreign Contamination Screen - Genome eXtractor) to screen and remove foreign contamination from genome assemblies

01200

fcsgx_report taxonomy_report log hits versions

fcsgx:

The NCBI Foreign Contamination Screen. Genomic cross-species aligner, for contamination detection.

GECCO is a fast and scalable method for identifying putative novel Biosynthetic Gene Clusters (BGCs) in genomic and metagenomic data using Conditional Random Fields (CRFs).

0120

genes features clusters gbk json versions

gecco:

Biosynthetic Gene Cluster prediction with Conditional Random Fields.

GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.

0123010101

bedpe bed versions

gridss:

GRIDSS: the Genomic Rearrangement IDentification Software Suite

GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.

01010101

vcf versions

gridss:

GRIDSS: the Genomic Rearrangement IDentification Software Suite

GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.

0123010101

bedpe bed versions

gridss:

GRIDSS: the Genomic Rearrangement IDentification Software Suite

GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.

0101

high_conf_sv all_sv versions

gridss:

GRIDSS: the Genomic Rearrangement IDentification Software Suite

GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.

0101

high_conf_sv all_sv versions

gridss:

GRIDSS: the Genomic Rearrangement IDentification Software Suite

Download database for GUNC detection of Chimerism and Contamination in Prokaryotic Genomes

0

db versions

gunc:

Python package for detection of chimerism and contamination in prokaryotic genomes.

Merging of CheckM and GUNC results in one summary table

012

tsv versions

gunc:

Python package for detection of chimerism and contamination in prokaryotic genomes.

Detection of Chimerism and Contamination in Prokaryotic Genomes

010

maxcss_level_tsv all_levels_tsv versions

gunc:

Python package for detection of chimerism and contamination in prokaryotic genomes.

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

inStrain is python program for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification

01000

profile snvs gene_info genome_info linkage mapping_info scaffold_info versions

instrain:

Calculation of strain-level metrics

miRDeep2 Mapper is a tool that prepares deep sequencing reads for downstream miRNA detection by collapsing reads, mapping them to a genome, and outputting the required files for miRNA discovery.

0101

outputs versions

mirdeep2:

miRDeep2 Mapper (mapper.pl) is part of the miRDeep2 suite. It collapses identical reads, maps them to a reference genome, and outputs both collapsed FASTA and ARF files for downstream miRNA detection and analysis.

miRDeep2 is a tool for identifying known and novel miRNAs in deep sequencing data by analyzing sequenced RNAs. It integrates the mapping of sequencing reads to the genome and predicts miRNA precursors and mature miRNAs.

012010123

outputs versions

mirdeep2:

miRDeep2 is a tool that discovers microRNA genes by analyzing sequenced RNAs. It includes three main scripts: miRDeep2.pl, mapper.pl, and quantifier.pl for comprehensive miRNA detection and quantification.

msisensor2 detection of MSI regions.

01234500

msi distribution somatic versions

msisensor2:

MSIsensor2 is a novel algorithm based machine learning, featuring a large upgrade in the microsatellite instability (MSI) detection for tumor only sequencing data, including Cell-Free DNA (cfDNA), Formalin-Fixed Paraffin-Embedded(FFPE) and other sample types. The original MSIsensor is specially designed for tumor/normal paired sequencing data.

msisensor2 detection of MSI regions.

00

scan versions

msisensor2:

MSIsensor2 is a novel algorithm based machine learning, featuring a large upgrade in the microsatellite instability (MSI) detection for tumor only sequencing data, including Cell-Free DNA (cfDNA), Formalin-Fixed Paraffin-Embedded(FFPE) and other sample types. The original MSIsensor is specially designed for tumor/normal paired sequencing data.

MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients with next generation sequencing data. It accepts the whole genome sequencing, whole exome sequencing and target region (panel) sequencing data as input

01234500

output_report output_dis output_germline output_somatic versions

msisensorpro:

Microsatellite Instability (MSI) detection using high-throughput sequencing data.

MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients with next generation sequencing data. It accepts the whole genome sequencing, whole exome sequencing and target region (panel) sequencing data as input

01

list versions

msisensorpro:

Microsatellite Instability (MSI) detection using high-throughput sequencing data.

A tool for peak detection in high-resolution profile data (Orbitrap or FTICR)

01

mzml versions

openms:

OpenMS is an open-source software C++ library for LC-MS data management and analyses

Automatically improve draft assemblies and find variation among strains, including large event detection

010120

improved_assembly vcf change_record tracks_bed tracks_wig versions

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

Accurate detection of short and long active ORFs using Ribo-seq data

01201

protocol bam_summary read_length_dist metagene_profile_5p metagene_profile_3p metagene_plots psite_offsets pos_wig neg_wig orfs versions

ribotricer:

Python package to detect translating ORF from Ribo-seq data

Accurate detection of short and long active ORFs using Ribo-seq data

012

candidate_orfs versions

ribotricer:

Python package to detect translating ORF from Ribo-seq data

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

0100

alignment trans_alignments multi_bed single_bed versions

segemehl:

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

Generate genome indices for segemehl align

0

index versions

segemehl:

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

Spotiflow, accurate and efficient spot detection with stereographic flow.

01

spots versions

uLTRA aligner - A wrapper around minimap2 to improve small exon detection - Map reads on genome

01001

bam versions

ultra:

Splice aligner of long transcriptomic reads to genome.

uLTRA aligner - A wrapper around minimap2 to improve small exon detection - Index gtf file for reads alignment

00

index versions

ultra:

Splice aligner of long transcriptomic reads to genome.

uLTRA aligner - A wrapper around minimap2 to improve small exon detection

0100

sam versions

ultra:

Splice aligner of long transcriptomic reads to genome.

Cluster sequences using a single-pass, greedy centroid-based clustering algorithm.

01

aln biom mothur otu bam out blast uc centroids clusters profile msa versions

vsearch:

VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)

Performs quality filtering and / or conversion of a FASTQ file to FASTA format.

01

fasta log versions

vsearch:

VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)

Taxonomic classification using the sintax algorithm.

010

tsv versions

vsearch:

VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)

Sort fasta entries by decreasing abundance (--sortbysize) or sequence length (--sortbylength).

010

fasta versions

vsearch:

VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)

Compare target sequences to fasta-formatted query sequences using global pairwise alignment.

010000

aln biom lca mothur otu sam tsv txt uc versions

vsearch:

VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)

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