Description

Taxonomic classification using the sintax algorithm.

Input

name:type
description
pattern

meta:map

Groovy Map containing query file information e.g. [ id:‘test’ ]

queryfasta:file

Query sequences in FASTA or FASTQ format

*.{fasta,fa,fna,faa,fastq,fq}

db:file

Reference database file in FASTA or UDB format

*

Output

name:type
description
pattern

tsv

meta:file

Results written to tab-delimited file

*.{tsv}

*.tsv:file

Results written to tab-delimited file

*.{tsv}

versions

versions.yml:file

File containing software versions

versions.yml

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 https://github.com/torognes/vsearch 10.7717/peerj.2584
included in
ampliseq
maintainer
Github user jtangrot
get in touch
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