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.

  • genomics 9
  • clustering 9
  • databases 9
  • searching 9
  • protein sequence 9
  • indexing 8
  • metagenomics 7
  • mmseqs2 7
  • hmmsearch 7
  • vsearch 6
  • database 4
  • align 4
  • taxonomic profiling 4
  • ncbi 4
  • public datasets 4
  • pypgx 4
  • fasta 3
  • fastq 3
  • index 3
  • classify 3
  • reporting 3
  • protein 3
  • sequences 3
  • population genetics 3
  • kmers 3
  • hmmer 3
  • antimicrobial peptides 3
  • amps 3
  • ampir 3
  • parsing 3
  • telomere 3
  • amplicon sequences 3
  • entrez 3
  • spaceranger 3
  • DRAMP 3
  • amplify 3
  • macrel 3
  • neubi 3
  • reference 2
  • variants 2
  • taxonomy 2
  • proteomics 2
  • structure 2
  • mkref 2
  • HMM 2
  • comparisons 2
  • ampgram 2
  • amptransformer 2
  • Pharmacogenetics 2
  • pharmacogenetics 2
  • vcf 1
  • alignment 1
  • assembly 1
  • sort 1
  • quality control 1
  • contamination 1
  • count 1
  • kmer 1
  • QC 1
  • phage 1
  • imaging 1
  • tsv 1
  • amr 1
  • openms 1
  • plot 1
  • blast 1
  • genotyping 1
  • spatial 1
  • sequence 1
  • plasmid 1
  • NCBI 1
  • query 1
  • microbiome 1
  • sourmash 1
  • taxonomic classification 1
  • SV 1
  • structural 1
  • containment 1
  • mzml 1
  • mlst 1
  • hidden Markov model 1
  • signature 1
  • FracMinHash sketch 1
  • blastp 1
  • metadata 1
  • dereplicate 1
  • sage 1
  • usearch 1
  • sintax 1
  • vsearch/sort 1
  • patterns 1
  • regex 1
  • InterProScan 1
  • lifestyle 1
  • MMseqs2 1
  • rank 1
  • homologs 1
  • nucleotide sequence 1
  • mass spectrometry 1
  • blat 1
  • controlstatistics 1
  • fastqfilter 1
  • vsearch/fastqfilter 1
  • vsearch/dereplicate 1
  • search engine 1
  • genomes on a tree 1
  • Hidden Markov Model 1
  • virulent 1
  • bacphlip 1
  • temperate 1
  • bioinformatics tools 1
  • Beautiful stand-alone HTML report 1
  • bam 0
  • genome 0
  • bed 0
  • gatk4 0
  • cram 0
  • sam 0
  • structural variants 0
  • variant calling 0
  • annotation 0
  • merge 0
  • filter 0
  • gff 0
  • bacteria 0
  • map 0
  • statistics 0
  • coverage 0
  • qc 0
  • gtf 0
  • download 0
  • nanopore 0
  • cnv 0
  • split 0
  • gfa 0
  • variant 0
  • MSA 0
  • k-mer 0
  • somatic 0
  • sentieon 0
  • classification 0
  • pacbio 0
  • convert 0
  • conversion 0
  • binning 0
  • quality 0
  • single-cell 0
  • VCF 0
  • copy number 0
  • ancient DNA 0
  • contigs 0
  • imputation 0
  • bedtools 0
  • phylogeny 0
  • graph 0
  • trimming 0
  • isoseq 0
  • gvcf 0
  • build 0
  • bcftools 0
  • sv 0
  • variation graph 0
  • bisulfite 0
  • table 0
  • consensus 0
  • illumina 0
  • picard 0
  • rnaseq 0
  • wgs 0
  • methylseq 0
  • bisulphite 0
  • methylation 0
  • bqsr 0
  • cna 0
  • compression 0
  • 5mC 0
  • antimicrobial resistance 0
  • mapping 0
  • long-read 0
  • metrics 0
  • stats 0
  • serotype 0
  • visualisation 0
  • demultiplex 0
  • scWGBS 0
  • WGBS 0
  • DNA methylation 0
  • haplotype 0
  • markduplicates 0
  • pairs 0
  • bins 0
  • depth 0
  • pangenome graph 0
  • base quality score recalibration 0
  • histogram 0
  • cluster 0
  • neural network 0
  • matrix 0
  • expression 0
  • aDNA 0
  • repeat 0
  • LAST 0
  • checkm 0
  • metagenome 0
  • completeness 0
  • genotype 0
  • palaeogenomics 0
  • machine learning 0
  • virus 0
  • archaeogenomics 0
  • bcf 0
  • mappability 0
  • damage 0
  • filtering 0
  • iCLIP 0
  • annotate 0
  • db 0
  • validation 0
  • samtools 0
  • bwa 0
  • biscuit 0
  • aligner 0
  • bisulfite sequencing 0
  • low-coverage 0
  • cooler 0
  • transcript 0
  • mag 0
  • transcriptome 0
  • decompression 0
  • gff3 0
  • segmentation 0
  • dedup 0
  • peaks 0
  • phasing 0
  • msa 0
  • kraken2 0
  • glimpse 0
  • bismark 0
  • example 0
  • evaluation 0
  • gene 0
  • newick 0
  • long reads 0
  • seqkit 0
  • ucsc 0
  • complexity 0
  • mags 0
  • umi 0
  • germline 0
  • pangenome 0
  • demultiplexing 0
  • scRNA-seq 0
  • splicing 0
  • differential 0
  • low frequency variant calling 0
  • prediction 0
  • mirna 0
  • bedGraph 0
  • cnvkit 0
  • prokaryote 0
  • short-read 0
  • multiple sequence alignment 0
  • report 0
  • single 0
  • gzip 0
  • snp 0
  • duplicates 0
  • deduplication 0
  • mitochondria 0
  • json 0
  • tumor-only 0
  • feature 0
  • antimicrobial resistance genes 0
  • fragment 0
  • gridss 0
  • MAF 0
  • text 0
  • visualization 0
  • detection 0
  • 3-letter genome 0
  • single cell 0
  • arg 0
  • summary 0
  • kallisto 0
  • de novo 0
  • call 0
  • clipping 0
  • wxs 0
  • mem 0
  • idXML 0
  • mutect2 0
  • view 0
  • antibiotic resistance 0
  • counts 0
  • extract 0
  • interval 0
  • indels 0
  • mpileup 0
  • deamination 0
  • adapters 0
  • merging 0
  • benchmark 0
  • csv 0
  • profiling 0
  • svtk 0
  • de novo assembly 0
  • isolates 0
  • ptr 0
  • riboseq 0
  • coptr 0
  • tabular 0
  • diversity 0
  • bin 0
  • cut 0
  • enrichment 0
  • genome assembler 0
  • bcl2fastq 0
  • fgbio 0
  • snps 0
  • read depth 0
  • CLIP 0
  • gsea 0
  • circrna 0
  • haplotypecaller 0
  • bedgraph 0
  • genmod 0
  • ranking 0
  • compress 0
  • peak-calling 0
  • diamond 0
  • deep learning 0
  • miscoding lesions 0
  • palaeogenetics 0
  • phylogenetic placement 0
  • ganon 0
  • interval_list 0
  • compare 0
  • archaeogenetics 0
  • hic 0
  • profile 0
  • bigwig 0
  • STR 0
  • paf 0
  • cat 0
  • chunk 0
  • ATAC-seq 0
  • FASTQ 0
  • concatenate 0
  • fastx 0
  • sample 0
  • sequencing 0
  • DNA sequencing 0
  • umitools 0
  • targeted sequencing 0
  • hybrid capture sequencing 0
  • copy number alteration calling 0
  • normalization 0
  • sketch 0
  • add 0
  • ont 0
  • resistance 0
  • union 0
  • xeniumranger 0
  • ancestry 0
  • isomir 0
  • microarray 0
  • retrotransposon 0
  • fungi 0
  • malt 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
  • matching 0
  • HiFi 0
  • preprocessing 0
  • happy 0
  • reports 0
  • notebook 0
  • bedpe 0
  • gatk4spark 0
  • somatic variants 0
  • ligate 0
  • mtDNA 0
  • windowmasker 0
  • pseudoalignment 0
  • krona chart 0
  • npz 0
  • variant_calling 0
  • mapper 0
  • typing 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
  • 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
  • subsample 0
  • UMI 0
  • informative sites 0
  • kinship 0
  • identity 0
  • relatedness 0
  • lossless 0
  • small indels 0
  • observations 0
  • shapeit 0
  • scores 0
  • zip 0
  • microbes 0
  • wig 0
  • arriba 0
  • rna 0
  • png 0
  • adapter trimming 0
  • angsd 0
  • ataqv 0
  • aln 0
  • abundance 0
  • bwameth 0
  • CRISPR 0
  • hi-c 0
  • pileup 0
  • bamtools 0
  • nucleotide 0
  • quality trimming 0
  • fusion 0
  • fai 0
  • intervals 0
  • converter 0
  • virulence 0
  • genome mining 0
  • chromosome 0
  • roh 0
  • prokaryotes 0
  • bracken 0
  • eukaryotes 0
  • combine 0
  • complement 0
  • cut up 0
  • cool 0
  • RNA-seq 0
  • remove 0
  • dump 0
  • image 0
  • mcmicro 0
  • prefetch 0
  • highly_multiplexed_imaging 0
  • atac-seq 0
  • image_analysis 0
  • cellranger 0
  • bakta 0
  • genomes 0
  • deeparg 0
  • C to T 0
  • chip-seq 0
  • gene expression 0
  • das tool 0
  • mkfastq 0
  • kraken 0
  • host 0
  • das_tool 0
  • clean 0
  • checkv 0
  • MaltExtract 0
  • phase 0
  • long terminal repeat 0
  • retrotransposons 0
  • pair 0
  • variation 0
  • pharokka 0
  • interactive 0
  • differential expression 0
  • function 0
  • HOPS 0
  • primer 0
  • authentication 0
  • orthology 0
  • parallelized 0
  • checksum 0
  • tree 0
  • transcriptomic 0
  • mudskipper 0
  • minhash 0
  • mash 0
  • edit distance 0
  • concordance 0
  • vdj 0
  • xz 0
  • archive 0
  • COBS 0
  • k-mer index 0
  • bloom filter 0
  • lofreq 0
  • gene set analysis 0
  • serogroup 0
  • barcode 0
  • krakenuniq 0
  • awk 0
  • krakentools 0
  • hlala_typing 0
  • Read depth 0
  • mask 0
  • leviosam2 0
  • lift 0
  • mapcounter 0
  • metamaps 0
  • hla_typing 0
  • ichorcna 0
  • taxon name 0
  • hlala 0
  • hla 0
  • genetics 0
  • functional analysis 0
  • taxids 0
  • regression 0
  • interactions 0
  • zlib 0
  • proteome 0
  • long terminal retrotransposon 0
  • polyA_tail 0
  • kma 0
  • screen 0
  • khmer 0
  • bustools 0
  • salmon 0
  • BAM 0
  • blastn 0
  • gene set 0
  • orf 0
  • immunoprofiling 0
  • refine 0
  • maximum likelihood 0
  • gstama 0
  • tama 0
  • iphop 0
  • trancriptome 0
  • instrain 0
  • windows 0
  • spatial_omics 0
  • megan 0
  • Duplication purging 0
  • small genome 0
  • de novo assembler 0
  • junctions 0
  • svdb 0
  • runs_of_homozygosity 0
  • polish 0
  • scaffold 0
  • contig 0
  • standardization 0
  • duplicate 0
  • taxonomic profile 0
  • graft 0
  • standardise 0
  • standardisation 0
  • otu tables 0
  • purge duplications 0
  • taxon tables 0
  • trim 0
  • library 0
  • preseq 0
  • adapter 0
  • demultiplexed reads 0
  • rtgtools 0
  • import 0
  • effect prediction 0
  • ancient dna 0
  • sequenzautils 0
  • switch 0
  • transformation 0
  • rename 0
  • shigella 0
  • seqtk 0
  • salmonella 0
  • varcal 0
  • fusions 0
  • soft-clipped clusters 0
  • scaffolding 0
  • snpeff 0
  • xenograft 0
  • snpsift 0
  • cancer genomics 0
  • fixmate 0
  • join 0
  • dict 0
  • collate 0
  • bam2fq 0
  • aggregate 0
  • artic 0
  • intersection 0
  • cnvnator 0
  • NRPS 0
  • msisensor-pro 0
  • micro-satellite-scan 0
  • tumor 0
  • proportionality 0
  • msi 0
  • instability 0
  • MSI 0
  • homoploymer 0
  • nucleotides 0
  • removal 0
  • multiallelic 0
  • small variants 0
  • rgfa 0
  • spatial_transcriptomics 0
  • resolve_bioscience 0
  • tnhaplotyper2 0
  • profiles 0
  • secondary metabolites 0
  • reformatting 0
  • GC content 0
  • mitochondrion 0
  • registration 0
  • simulate 0
  • ped 0
  • RNA-Seq 0
  • variant pruning 0
  • bfiles 0
  • distance 0
  • vcflib 0
  • vg 0
  • concat 0
  • read-group 0
  • tbi 0
  • intersect 0
  • nextclade 0
  • GPU-accelerated 0
  • normalize 0
  • norm 0
  • scatter 0
  • reheader 0
  • antismash 0
  • SimpleAF 0
  • antibiotics 0
  • graph layout 0
  • RiPP 0
  • image_processing 0
  • comparison 0
  • Streptococcus pneumoniae 0
  • sequence analysis 0
  • microbial 0
  • frame-shift correction 0
  • deconvolution 0
  • bayesian 0
  • long-read sequencing 0
  • CNV 0
  • cvnkit 0
  • calling 0
  • merge mate pairs 0
  • reads merging 0
  • short reads 0
  • doublets 0
  • gwas 0
  • realignment 0
  • unaligned 0
  • ome-tif 0
  • gatk 0
  • joint genotyping 0
  • eCLIP 0
  • repeats 0
  • recombination 0
  • panelofnormals 0
  • evidence 0
  • estimation 0
  • MCMICRO 0
  • mirdeep2 0
  • RNA sequencing 0
  • smrnaseq 0
  • filtermutectcalls 0
  • interval list 0
  • allele-specific 0
  • anndata 0
  • UMIs 0
  • parse 0
  • fasterq-dump 0
  • sra-tools 0
  • eigenstrat 0
  • validate 0
  • samplesheet 0
  • format 0
  • eido 0
  • mRNA 0
  • deseq2 0
  • rna-seq 0
  • structural-variant calling 0
  • metagenomes 0
  • heatmap 0
  • random forest 0
  • regions 0
  • settings 0
  • nanostring 0
  • duplex 0
  • repeat_expansions 0
  • fetch 0
  • GEO 0
  • metagenomic 0
  • identifier 0
  • gene labels 0
  • expansionhunterdenovo 0
  • nacho 0
  • screening 0
  • cleaning 0
  • tab 0
  • trgt 0
  • correction 0
  • emboss 0
  • corrupted 0
  • cnv calling 0
  • single cells 0
  • genome bins 0
  • genomad 0
  • baf 0
  • ChIP-seq 0
  • gem 0
  • allele 0
  • vcflib/vcffixup 0
  • umicollapse 0
  • trimfq 0
  • nanopore sequencing 0
  • scRNA-Seq 0
  • morphology 0
  • resegment 0
  • AC/NS/AF 0
  • files 0
  • relabel 0
  • hostile 0
  • Pacbio 0
  • adapterremoval 0
  • cell segmentation 0
  • upd 0
  • uniparental 0
  • disomy 0
  • snv 0
  • downsample 0
  • downsample bam 0
  • antimicrobial reistance 0
  • mkarv 0
  • decontamination 0
  • atlas 0
  • contiguate 0
  • scanpy 0
  • Mycobacterium tuberculosis 0
  • chromosomal rearrangements 0
  • eucaryotes 0
  • extension 0
  • coding 0
  • cds 0
  • transcroder 0
  • sequencing adapters 0
  • bedgraphtobigwig 0
  • rna velocity 0
  • bigbed 0
  • bedtobigbed 0
  • genepred 0
  • refflat 0
  • gtftogenepred 0
  • ucsc/liftover 0
  • cobra 0
  • metagenome assembler 0
  • vcf2db 0
  • human removal 0
  • subsample bam 0
  • lua 0
  • gemini 0
  • logFC 0
  • pangenome-scale 0
  • all versus all 0
  • mashmap 0
  • wavefront 0
  • whamg 0
  • wham 0
  • bwameme 0
  • HLA 0
  • copy-number 0
  • grabix 0
  • bwamem2 0
  • copy number analysis 0
  • subsetting 0
  • pile up 0
  • barcodes 0
  • doublet_detection 0
  • gender determination 0
  • ribosomal 0
  • copy number alterations 0
  • copy number variation 0
  • yahs 0
  • long read alignment 0
  • significance statistic 0
  • maf 0
  • construct 0
  • cellsnp 0
  • toml 0
  • nuclear segmentation 0
  • vcfbreakmulti 0
  • uniq 0
  • deduplicate 0
  • VCFtools 0
  • verifybamid 0
  • DNA contamination estimation 0
  • import segmentation 0
  • graph projection to vcf 0
  • solo 0
  • scvi 0
  • guidetree 0
  • http(s) 0
  • extractunbinned 0
  • linkbins 0
  • utility 0
  • p-value 0
  • grea 0
  • regtools 0
  • plotting 0
  • paired reads re-pairing 0
  • SMN1 0
  • SMN2 0
  • POA 0
  • sniffles 0
  • core 0
  • snippy 0
  • dist 0
  • hashing-based deconvoltion 0
  • fix 0
  • autofluorescence 0
  • malformed 0
  • partitioning 0
  • chip 0
  • dbnsfp 0
  • predictions 0
  • updatedata 0
  • run 0
  • pdb 0
  • SNPs 0
  • CRAM 0
  • gnu 0
  • busco 0
  • sha256 0
  • relative coverage 0
  • catpack 0
  • rare variants 0
  • error 0
  • transposable element 0
  • de-novo 0
  • Computational Immunology 0
  • longread 0
  • generic 0
  • sliding window 0
  • 256 bit 0
  • Bioinformatics Tools 0
  • Immune Deconvolution 0
  • shinyngs 0
  • doublet 0
  • exploratory 0
  • boxplot 0
  • density 0
  • features 0
  • coreutils 0
  • hamming-distance 0
  • invariant 0
  • fast5 0
  • recovery 0
  • ATLAS 0
  • detecting svs 0
  • short-read sequencing 0
  • lexogen 0
  • sylph 0
  • mgi 0
  • sequencing_bias 0
  • svtk/baftest 0
  • baftest 0
  • countsvtypes 0
  • genotype-based demultiplexing 0
  • variantcalling 0
  • donor deconvolution 0
  • rdtest2vcf 0
  • rdtest 0
  • split_kmers 0
  • vcf2bed 0
  • leafcutter 0
  • decompress 0
  • post mortem damage 0
  • polya tail 0
  • mapad 0
  • bias 0
  • sccmec 0
  • constant 0
  • overlap-based merging 0
  • cycif 0
  • background 0
  • single-stranded 0
  • ancientDNA 0
  • rRNA 0
  • ribosomal RNA 0
  • check 0
  • authentict 0
  • block substitutions 0
  • decomposeblocksub 0
  • signatures 0
  • streptococcus 0
  • hash sketch 0
  • identity-by-descent 0
  • fracminhash sketch 0
  • read group 0
  • paired reads merging 0
  • translation 0
  • spatype 0
  • functional enrichment 0
  • spa 0
  • droplet based single cells 0
  • geo 0
  • c to t 0
  • adna 0
  • script 0
  • standard 0
  • clahe 0
  • install 0
  • joint-genotyping 0
  • genotypegvcf 0
  • realign 0
  • model 0
  • svg 0
  • xml 0
  • circular 0
  • spot 0
  • introns 0
  • java 0
  • AMPs 0
  • parallel 0
  • hashing-based deconvolution 0
  • Staphylococcus aureus 0
  • plastid 0
  • tag2tag 0
  • resfinder 0
  • resistance genes 0
  • haplotag 0
  • quality check 0
  • raw 0
  • association 0
  • bam2fastx 0
  • bam2fastq 0
  • immcantation 0
  • airrseq 0
  • immunoinformatics 0
  • co-orthology 0
  • homology 0
  • sequence similarity 0
  • spectral clustering 0
  • comparative genomics 0
  • microRNA 0
  • size 0
  • deep variant 0
  • mutect 0
  • idx 0
  • affy 0
  • refresh 0
  • cram-size 0
  • Staging 0
  • staging 0
  • transform 0
  • gaps 0
  • tags 0
  • genetic sex 0
  • multiqc 0
  • reference-independent 0
  • antimicrobial peptide prediction 0
  • nanoq 0
  • multi-tool 0
  • predict 0
  • amp 0
  • redundant 0
  • hardy-weinberg 0
  • hwe statistics 0
  • hwe equilibrium 0
  • genotype likelihood 0
  • Read filters 0
  • collapse 0
  • WGS 0
  • cgMLST 0
  • liftover 0
  • probabilistic realignment 0
  • extraction 0
  • seqfu 0
  • n50 0
  • cell_type_identification 0
  • featuretable 0
  • Read trimming 0
  • impute-info 0
  • python 0
  • parquet 0
  • functional 0
  • orthogroup 0
  • parser 0
  • dbsnp 0
  • standardize 0
  • orthologs 0
  • quarto 0
  • Illumina 0
  • uniques 0
  • r 0
  • distance-based 0
  • coexpression 0
  • correlation 0
  • corpcor 0
  • assay 0
  • phylogenetics 0
  • machine_learning 0
  • drug categorization 0
  • Read report 0
  • cell_phenotyping 0
  • minimum_evolution 0
  • structural variant 0
  • GWAS 0
  • Escherichia coli 0
  • mygene 0
  • elprep 0
  • chloroplast 0
  • confidence 0
  • alr 0
  • clr 0
  • elfasta 0
  • boxcox 0
  • retrieval 0
  • nucleotide content 0
  • tnscope 0
  • AT content 0
  • cell_barcodes 0
  • nucBed 0
  • bclconvert 0
  • tag 0
  • prior knowledge 0
  • propd 0
  • transcription factors 0
  • Read coverage histogram 0
  • biological activity 0
  • bgen 0
  • groupby 0
  • targz 0
  • workflow_mode 0
  • admixture 0
  • proteus 0
  • readproteingroups 0
  • reference panels 0
  • eigenvectors 0
  • hicPCA 0
  • sliding 0
  • quality_control 0
  • snakemake 0
  • workflow 0
  • 10x 0
  • regulatory network 0
  • createreadcountpanelofnormals 0
  • copyratios 0
  • denoisereadcounts 0
  • readwriter 0
  • dnamodelapply 0
  • dnascope 0
  • go 0
  • emoji 0
  • source tracking 0
  • omics 0
  • tarball 0
  • mass_error 0
  • array_cgh 0
  • ancestral alleles 0
  • derived alleles 0
  • tnfilter 0
  • nuclear contamination estimate 0
  • paraphase 0
  • telseq 0
  • selector 0
  • stardist 0
  • ATACseq 0
  • cytosure 0
  • post Post-processing 0
  • vector 0
  • gprofiler2 0
  • gost 0
  • variant-calling 0
  • case/control 0
  • poolseq 0
  • rad 0
  • site frequency spectrum 0
  • allele counts 0
  • tar 0
  • Bayesian 0
  • reverse complement 0
  • simulation 0
  • hmmfetch 0
  • decompose 0
  • translate 0
  • structural-variants 0
  • transmembrane 0
  • jvarkit 0
  • genome graph 0
  • setgt 0
  • tnseq 0
  • shift 0
  • scimap 0
  • spatial_neighborhoods 0
  • decoy 0
  • associations 0
  • htseq 0
  • rrna 0
  • installation 0
  • sompy 0
  • doCounts 0
  • ATACshift 0
  • peak picking 0
  • mgf 0
  • amino acid 0
  • sex determination 0
  • genome manipulation 0
  • genome statistics 0
  • crispr 0
  • gget 0
  • low coverage 0
  • antibody capture 0
  • antigen capture 0
  • Sample 0
  • Haplotypes 0
  • Imputation 0
  • joint-variant-calling 0
  • GNU 0
  • merge compare 0
  • multiomics 0
  • gfastats 0
  • tama_collapse.py 0
  • mkvdjref 0
  • gene model 0
  • TAMA 0
  • gstama/merge 0
  • gstama/polyacleanup 0
  • GTDB taxonomy 0
  • genome taxonomy database 0
  • archaea 0
  • cellpose 0
  • gunc 0
  • gunzip 0
  • gvcftools 0
  • extract_variants 0
  • genome summary 0
  • qa 0
  • hifi 0
  • variantrecalibrator 0
  • reblockgvcf 0
  • revert 0
  • selectvariants 0
  • shiftchain 0
  • shiftfasta 0
  • shiftintervals 0
  • site depth 0
  • splitcram 0
  • splitintervals 0
  • svannotate 0
  • svcluster 0
  • variantfiltration 0
  • recalibration model 0
  • gawk 0
  • quality assurnce 0
  • txt 0
  • file parsing 0
  • bgc 0
  • chromosome_visualization 0
  • duplicate removal 0
  • genome profile 0
  • compound 0
  • models 0
  • chromap 0
  • genome size 0
  • genome heterozygosity 0
  • repeat content 0
  • Salmonella Typhi 0
  • Mykrobe 0
  • extractvariants 0
  • abricate 0
  • printreads 0
  • Salmonella enterica 0
  • population genomics 0
  • postprocessing 0
  • interproscan 0
  • genomic islands 0
  • insertion 0
  • jasminesv 0
  • jasmine 0
  • Python 0
  • Jupyter 0
  • jupytext 0
  • papermill 0
  • tblastn 0
  • subtyping 0
  • kallisto/index 0
  • pixel_classification 0
  • quant 0
  • sorted 0
  • digital normalization 0
  • k-mer counting 0
  • effective genome size 0
  • Klebsiella 0
  • pneumoniae 0
  • file manipulation 0
  • kegg 0
  • kofamscan 0
  • combining 0
  • bioawk 0
  • unionBedGraphs 0
  • subtract 0
  • probability_maps 0
  • pixel classification 0
  • amrfinderplus 0
  • gccounter 0
  • fARGene 0
  • rgi 0
  • ibd 0
  • hbd 0
  • beagle 0
  • mitochondrial 0
  • haplogroups 0
  • Assembly 0
  • Haemophilus influenzae 0
  • haplotype resolution 0
  • domains 0
  • compartments 0
  • topology 0
  • calder2 0
  • readcounter 0
  • multicut 0
  • cadd 0
  • reformat 0
  • HMMER 0
  • hmtnote 0
  • annotations 0
  • pos 0
  • haemophilus 0
  • panel_of_normals 0
  • IDR 0
  • igv 0
  • igv.js 0
  • js 0
  • genome browser 0
  • printsvevidence 0
  • preprocessintervals 0
  • spliced 0
  • SRA 0
  • TMA dearray 0
  • UNet 0
  • mcool 0
  • genomic bins 0
  • makebins 0
  • str 0
  • faqcs 0
  • antibiotic resistance genes 0
  • ARGs 0
  • ANI 0
  • enzyme 0
  • digest 0
  • cload 0
  • ENA 0
  • Cores 0
  • public 0
  • cooler/balance 0
  • consensus sequence 0
  • duplexumi 0
  • subcontigs 0
  • groupreads 0
  • unmapped 0
  • ubam 0
  • zipperbams 0
  • nucleotide composition 0
  • concoct 0
  • single molecule 0
  • generate 0
  • random 0
  • Segmentation 0
  • cache 0
  • lint 0
  • PEP 0
  • corrrelation 0
  • scatterplot 0
  • cumulative coverage 0
  • paired-end 0
  • pcr duplicates 0
  • cutesv 0
  • blastx 0
  • gct 0
  • segment 0
  • cls 0
  • duphold 0
  • structural variation 0
  • depth information 0
  • escherichia coli 0
  • schema 0
  • percent on target 0
  • pep 0
  • eigenstratdatabasetools 0
  • eklipse 0
  • na 0
  • version 0
  • circos 0
  • deletion 0
  • custom 0
  • split by chromosome 0
  • embl 0
  • genbank 0
  • swissprot 0
  • Streptococcus pyogenes 0
  • endogenous DNA 0
  • partition histograms 0
  • fq 0
  • postprocessgermlinecnvcalls 0
  • genomicsdb 0
  • dragstr 0
  • condensedepthevidence 0
  • createsequencedictionary 0
  • polymut 0
  • createsomaticpanelofnormals 0
  • determinegermlinecontigploidy 0
  • duplication metrics 0
  • estimatelibrarycomplexity 0
  • filterintervals 0
  • splice 0
  • filtervarianttranches 0
  • tranche filtering 0
  • gatherbqsrreports 0
  • genomicsdbimport 0
  • short variant discovery 0
  • jointgenotyping 0
  • panelofnormalscreation 0
  • germline contig ploidy 0
  • germlinecnvcaller 0
  • germlinevariantsites 0
  • getpileupsumaries 0
  • readcountssummary 0
  • indexfeaturefile 0
  • learnreadorientationmodel 0
  • readorientationartifacts 0
  • leftalignandtrimvariants 0
  • mergebamalignment 0
  • mutectstats 0
  • snvs 0
  • composestrtablefile 0
  • combinegvcfs 0
  • rust 0
  • targets 0
  • variant caller 0
  • target 0
  • somatic variant calling 0
  • germline variant calling 0
  • bacterial variant calling 0
  • export 0
  • bootstrapping 0
  • UShER 0
  • gamma 0
  • gene-calling 0
  • gangstr 0
  • antitarget 0
  • access 0
  • heattree 0
  • annotateintervals 0
  • polymorphic 0
  • cmseq 0
  • protein coding genes 0
  • polymorphic sites 0
  • variant quality score recalibration 0
  • vqsr 0
  • asereadcounter 0
  • bedtointervallist 0
  • calculatecontamination 0
  • cross-samplecontamination 0
  • getpileupsummaries 0
  • calibratedragstrmodel 0
  • cnnscorevariants 0
  • collectreadcounts 0
  • collectsvevidence 0
  • reorder 0
  • train 0
  • induce 0
  • genomic intervals 0
  • microscopy 0
  • background_correction 0
  • contact 0
  • pretext 0
  • jpg 0
  • bmp 0
  • contact maps 0
  • gene finding 0
  • illumiation_correction 0
  • element 0
  • intervals coverage 0
  • trimBam 0
  • bamUtil 0
  • normal database 0
  • pmdtools 0
  • panel of normals 0
  • cutoff 0
  • haplotype purging 0
  • duplicate purging 0
  • false duplications 0
  • assembly curation 0
  • Haplotype purging 0
  • False duplications 0
  • Assembly curation 0
  • track 0
  • purging 0
  • bamtools/split 0
  • yaml 0
  • quast 0
  • porechop_abi 0
  • variant genetic 0
  • subsampling 0
  • csRNA-seq 0
  • mate-pair 0
  • liftovervcf 0
  • pcr 0
  • picard/renamesampleinvcf 0
  • sortvcf 0
  • deletions 0
  • insertions 0
  • tandem duplications 0
  • CoPRO 0
  • GRO-cap 0
  • PRO-cap 0
  • CAGE 0
  • NETCAGE 0
  • RAMPAGE 0
  • STRIPE-seq 0
  • scoring 0
  • PRO-seq 0
  • GRO-seq 0
  • genetic 0
  • deduping 0
  • smaller fastqs 0
  • clumping fastqs 0
  • exclude 0
  • variant identifiers 0
  • subset 0
  • indep 0
  • indep pairwise 0
  • recode 0
  • whole genome association 0
  • identifiers 0
  • neighbour-joining 0
  • long uncorrected reads 0
  • csi 0
  • scramble 0
  • cluster analysis 0
  • clusteridentifier 0
  • peak-caller 0
  • cut&tag 0
  • cut&run 0
  • chromatin 0
  • seacr 0
  • assembly-binning 0
  • applyvarcal 0
  • VQSR 0
  • variant recalibration 0
  • subseq 0
  • read pairs 0
  • grep 0
  • sequence headers 0
  • sertotype 0
  • interleave 0
  • header 0
  • seq 0
  • selection 0
  • random draw 0
  • pseudohaploid 0
  • pseudodiploid 0
  • freqsum 0
  • bam2seqz 0
  • gc_wiggle 0
  • readgroup 0
  • paired 0
  • rhocall 0
  • pedfilter 0
  • R 0
  • bamstat 0
  • bamtools/convert 0
  • strandedness 0
  • experiment 0
  • read_pairs 0
  • fragment_size 0
  • inner_distance 0
  • read distribution 0
  • sequence-based 0
  • mapping-based 0
  • mouse 0
  • integrity 0
  • rtg 0
  • rocplot 0
  • repair 0
  • rtg-tools 0
  • salsa 0
  • salsa2 0
  • LCA 0
  • Ancestor 0
  • multimapper 0
  • flagstat 0
  • sambamba 0
  • duplicate marking 0
  • amplicon 0
  • ampliconclip 0
  • calmd 0
  • faidx 0
  • insert size 0
  • hybrid-selection 0
  • phylogenetic composition 0
  • adapter removal 0
  • contour map 0
  • chunking 0
  • mass-spectroscopy 0
  • mcr-1 0
  • MD5 0
  • 128 bit 0
  • megahit 0
  • denovo 0
  • debruijn 0
  • daa 0
  • rma6 0
  • Neisseria meningitidis 0
  • k-mer frequency 0
  • 3D heat map 0
  • Merqury 0
  • maskfasta 0
  • jaccard 0
  • assembly evaluation 0
  • smudgeplot 0
  • ploidy 0
  • unionsum 0
  • metaphlan 0
  • methylation bias 0
  • mbias 0
  • assembler 0
  • de Bruijn 0
  • overlap 0
  • microrna 0
  • getfasta 0
  • target prediction 0
  • metagenome-assembled genomes 0
  • maxbin2 0
  • reference genome 0
  • sgRNA 0
  • collapsing 0
  • legionella 0
  • clinical 0
  • pneumophila 0
  • limma 0
  • Listeria monocytogenes 0
  • slopBed 0
  • lofreq/call 0
  • lofreq/filter 0
  • qualities 0
  • AMP 0
  • peptide prediction 0
  • bases 0
  • functional genomics 0
  • CRISPR-Cas9 0
  • representations 0
  • maximum-likelihood 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
  • mash/sketch 0
  • reduced 0
  • mitochondrial genome 0
  • genomecov 0
  • illumina datasets 0
  • select 0
  • tumor/normal 0
  • hla-typing 0
  • ILP 0
  • HLA-I 0
  • block-compressed 0
  • update header 0
  • PCR/optical duplicates 0
  • flip 0
  • upper-triangular matrix 0
  • ligation junctions 0
  • pairtools 0
  • pairstools 0
  • restriction fragments 0
  • BCF 0
  • graph formats 0
  • paragraph 0
  • graphs 0
  • pbbam 0
  • pbmerge 0
  • subreads 0
  • pbp 0
  • pair-end 0
  • read 0
  • pedigrees 0
  • motif 0
  • ChIP-Seq 0
  • phantom peaks 0
  • prophage 0
  • identification 0
  • graph viz 0
  • graph unchopping 0
  • closest 0
  • contaminant 0
  • bamtobed 0
  • mosdepth 0
  • otu table 0
  • sorting 0
  • microsatellite instability 0
  • scan 0
  • mtnucratio 0
  • ratio 0
  • autozygosity 0
  • mitochondrial to nuclear ratio 0
  • GATK UnifiedGenotyper 0
  • SNP table 0
  • cancer genome 0
  • graph stats 0
  • somatic structural variations 0
  • mobile element insertions 0
  • sequencing summary 0
  • NextGenMap 0
  • ngm 0
  • Neisseria gonorrhoeae 0
  • gender 0
  • homozygosity 0
  • biallelic 0
  • graph construction 0
  • graph drawing 0
  • squeeze 0
  • odgi 0
  • combine graphs 0
  • prepare 0

A tool to parse and summarise results from antimicrobial peptides tools and present functional classification.

0100

sample_dir txt csv faa summary_csv summary_html log results_db results_db_dmnd results_db_fasta results_db_tsv versions

A submodule that merges all output summary tables from ampcombi/parsetables in one summary file.

0

tsv log versions

ampcombi2/complete:

This merges the per sample AMPcombi summaries generated by running 'ampcombi2/parsetables'.

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.

A bacteriophage lifestyle prediction tool

01

bacphlip_results hmmsearch_results versions

BLASTP (Basic Local Alignment Search Tool- Protein) compares an amino acid (protein) query sequence against a protein database

01010

xml tsv csv versions

blast:

BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit.

Queries a sequence subject

0101

psl versions

Searches a term in a public NCBI database

010

xml versions

entrezdirect:

Entrez Direct (EDirect) is a method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.

Queries an NCBI database using Unique Identifier(s)

0120

xml versions

entrezdirect:

Entrez Direct (EDirect) is a method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.

Queries an NCBI database using an UID

01000

txt versions

entrezdirect:

Entrez Direct (EDirect) is a method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.

Run FCS-GX on assembled genomes. The contigs of the assembly are searched against a reference database excluding the given taxid.

010

fcs_gx_report taxonomy_report versions

fcs:

"The Foreign Contamination Screening (FCS) tool rapidly detects contaminants from foreign organisms in genome assemblies to prepare your data for submission. Therefore, the submission process to NCBI is faster and fewer contaminated genomes are submitted. This reduces errors in analyses and conclusions, not just for the original data submitter but for all subsequent users of the assembly."

Create a database from protein structures

01

db versions

foldseek:

Foldseek: fast and accurate protein structure search

Search for protein structural hits against a foldseek database of protein structures

0101

aln versions

foldseek:

Foldseek: fast and accurate protein structure search

Query metadata for any taxon across the tree of life.

012

taxonsearch versions

goat:

goat-cli is a command line interface to query the Genomes on a Tree Open API.

create an hmm profile from a multiple sequence alignment

010

hmm hmmbuildout versions

hmmer:

Biosequence analysis using profile hidden Markov models

R script that scores output from multiple runs of hmmer/hmmsearch

01

hmmrank versions

hmmer:

Biosequence analysis using profile hidden Markov models

R:

A Language and Environment for Statistical Computing

Tidyverse:

Tidyverse: R packages for data science

search profile(s) against a sequence database

012345

output alignments target_summary domain_summary versions

hmmer:

Biosequence analysis using profile hidden Markov models

Merge search results from multiple databases.

01

result versions

kmcp:

Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping

Generate taxonomic profile from search results

010

profile versions

kmcp:

Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping

Search sequences against database

010

result versions

kmcp:

Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping

Cluster sequences using MMSeqs2 cluster.

01

db_cluster versions

mmseqs:

MMseqs2: ultra fast and sensitive sequence search and clustering suite

Create an MMseqs database from an existing FASTA/Q file

01

db versions

mmseqs:

MMseqs2: ultra fast and sensitive sequence search and clustering suite

Creates sequence index for mmseqs database

01

db_indexed versions

mmseqs:

MMseqs2: ultra fast and sensitive sequence search and clustering suite

Create a tsv file from a query and a target database as well as the result database

010101

tsv versions

mmseqs:

MMseqs2: ultra fast and sensitive sequence search and clustering suite

Download an mmseqs-formatted database

0

database versions

mmseqs:

MMseqs2: ultra fast and sensitive sequence search and clustering suite

Searches for the sequences of a fasta file in a database using MMseqs2

0101

tsv versions

mmseqs:

MMseqs2: ultra fast and sensitive sequence search and clustering suite

Cluster sequences in linear time using MMSeqs2 linclust.

01

db_cluster versions

mmseqs:

MMseqs2: ultra fast and sensitive sequence search and clustering suite

Search and calculate a score for similar sequences in a query and a target database.

0101

db_search versions

mmseqs:

MMseqs2: ultra fast and sensitive sequence search and clustering suite

Computes the lowest common ancestor by identifying the query sequence homologs against the target database.

010

db_taxonomy versions

mmseqs:

MMseqs2: ultra fast and sensitive sequence search and clustering suite

Conversion of expandable profile to databases to the MMseqs2 databases format

0

db_exprofile versions

mmseqs:

MMseqs2: ultra fast and sensitive sequence search and clustering suite

Aggregate results from bioinformatics analyses across many samples into a single report

000000

report data plots versions

multiqc:

MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.

Annotates MS/MS spectra using Comet.

012

idxml pin versions

openms:

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

Compute summary statistics for control gene from BAM files.

01200

control_stats versions

pypgx:

A Python package for pharmacogenomics research

Call SNVs/indels from BAM files for all target genes.

0120100

vcf tbi versions

pypgx:

A Python package for pharmacogenomics research

Prepare a depth of coverage file for all target genes with SV from BAM files.

01200

coverage versions

pypgx:

A Python package for pharmacogenomics research

PyPGx pharmacogenomics genotyping pipeline for NGS data.

012345010

results cnv_calls consolidated_variants versions

pypgx:

A Python package for pharmacogenomics research

ripgrep recursively searches directories for a regex pattern

0100

txt versions

pigz:

Parallel implementation of the gzip algorithm.

sage is a search software for proteomics data

010101

results_tsv results_json results_pin versions tmt_tsv lfq_tsv

sageproteomics:

Proteomics searching so fast it feels like magic.

Search a metagenome sourmash signature against one or many reference databases and return the minimum set of genomes that contain the k-mers in the metagenome.

0100000

result unassigned matches prefetch prefetchcsv versions

sourmash:

Compute and compare FracMinHash signatures for DNA data sets.

Module to use the 10x Space Ranger pipeline to process 10x spatial transcriptomics data

0123456700

outs versions

spaceranger:

Visium Spatial Gene Expression is a next-generation molecular profiling solution for classifying tissue based on total mRNA. Space Ranger is a set of analysis pipelines that process Visium Spatial Gene Expression data with brightfield and fluorescence microscope images. Space Ranger allows users to map the whole transcriptome in formalin fixed paraffin embedded (FFPE) and fresh frozen tissues to discover novel insights into normal development, disease pathology, and clinical translational research. Space Ranger provides pipelines for end to end analysis of Visium Spatial Gene Expression experiments.

Module to build a filtered GTF needed by the 10x Genomics Space Ranger tool. Uses the spaceranger mkgtf command.

0

gtf versions

spaceranger:

Visium Spatial Gene Expression is a next-generation molecular profiling solution for classifying tissue based on total mRNA. Space Ranger is a set of analysis pipelines that process Visium Spatial Gene Expression data with brightfield and fluorescence microscope images. Space Ranger allows users to map the whole transcriptome in formalin fixed paraffin embedded (FFPE) and fresh frozen tissues to discover novel insights into normal development, disease pathology, and clinical translational research. Space Ranger provides pipelines for end to end analysis of Visium Spatial Gene Expression experiments.

Module to build the reference needed by the 10x Genomics Space Ranger tool. Uses the spaceranger mkref command.

000

reference versions

spaceranger:

Visium Spatial Gene Expression is a next-generation molecular profiling solution for classifying tissue based on total mRNA. Space Ranger is a set of analysis pipelines that process Visium Spatial Gene Expression data with brightfield and fluorescence microscope images. Space Ranger allows users to map the whole transcriptome in formalin fixed paraffin embedded (FFPE) and fresh frozen tissues to discover novel insights into normal development, disease pathology, and clinical translational research. Space Ranger provides pipelines for end to end analysis of Visium Spatial Gene Expression experiments.

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

01

results_xlsx summary_tsv detailed_summary_tsv resfinder_tsv plasmidfinder_tsv mlst_tsv settings_txt pointfinder_tsv versions

staramr:

Scan genome contigs against the ResFinder and PointFinder databases. In order to use the PointFinder databases, you will have to add --pointfinder-organism ORGANISM to the ext.args options.

Identify chromosomal rearrangements.

0120101

vcf ploidy versions

sv:

Search for structural variants.

tidk explore attempts to find the simple telomeric repeat unit in the genome provided. It will report this repeat in its canonical form (e.g. TTAGG -> AACCT).

01

explore_tsv top_sequence versions

tidk:

tidk is a toolkit to identify and visualise telomeric repeats in genomes

Plots telomeric repeat frequency against sliding window location using data produced by tidk/search

01

svg versions

tidk:

tidk is a toolkit to identify and visualise telomeric repeats in genomes

Searches a genome for a telomere string such as TTAGGG

010

tsv bedgraph versions

tidk:

tidk is a toolkit to identify and visualise telomeric repeats in genomes

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)

Merge strictly identical sequences contained in filename. Identical sequences are defined as having the same length and the same string of nucleotides (case insensitive, T and U are considered the same).

01

fasta clustering log versions

vsearch:

A versatile open source tool for metagenomics (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)

Click here to trigger an update.