Description

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

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information e.g. [ id:'test' ]

fasta (file)

Sequences to cluster in FASTA format

*.{fasta,fa,fasta.gz,fa.gz}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'test' ]

aln (file)

Results in pairwise alignment format

*.aln.gz

biom (file)

Results in an OTU table in the biom version 1.0 file format

*.biom.gz

mothur (file)

Results in an OTU table in the mothur ’shared’ tab-separated plain text file format

*.mothur.tsv.gz

otu (file)

Results in an OTU table in the classic tab-separated plain text format

*.otu.tsv.gz

bam (file)

Results written in bam format

*.bam

out (file)

Results in tab-separated output, columns defined by user

*.out.tsv.gz

blast (file)

Tab delimited results in blast-like tabular format

*.blast.tsv.gz

uc (file)

Tab delimited results in a uclust-like format with 10 columns

*.uc.gz

versions (file)

File containing software versions

versions.yml
included in
crisprseq
author
Github user mirpedrol
get in touch
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Tools

vsearch
GPL v3-or-later OR BSD-2-clause

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)

github.com/torognes/vsearch github.com/torognes/vsearch/releases/download/v2.21.1/vsearch_manual.pdf https://github.com/torognes/vsearch10.7717/peerj.2584