Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

queryfasta{:bash}

:file

Query sequences in FASTA format

*.{fasta,fa,fna,faa}

db{:bash}

:file

Reference database file in FASTA or UDB format

*

idcutoff{:bash}

:float

Reject the sequence match if the pairwise identity is lower than the given id cutoff value (value ranging from 0.0 to 1.0 included)

outoption{:bash}

:string

Specify the type of output file to be generated by selecting one of the vsearch output file options

alnout|biomout|blast6out|mothur_shared_out|otutabout|samout|uc|userout|lcaout

user_columns{:bash}

:string

If using the userout option, specify which columns to include in output, with fields separated with + (e.g. query+target+id). See USEARCH manual for valid options. For other output options, use an empty string.

Output

name:type
description
pattern

aln{:bash}

meta{:bash}

:file

Results in pairwise alignment format

*.{aln}

*.aln{:bash}

:file

Results in pairwise alignment format

*.{aln}

biom{:bash}

meta{:bash}

:file

Results in pairwise alignment format

*.{aln}

*.biom{:bash}

:file

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

*.{biom}

lca{:bash}

meta{:bash}

:file

Results in pairwise alignment format

*.{aln}

*.lca{:bash}

:file

Last common ancestor (LCA) information about the hits of each query in tab-separated format

*.{lca}

mothur{:bash}

meta{:bash}

:file

Results in pairwise alignment format

*.{aln}

*.mothur{:bash}

:file

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

*.{mothur}

otu{:bash}

meta{:bash}

:file

Results in pairwise alignment format

*.{aln}

*.otu{:bash}

:file

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

*.{otu}

sam{:bash}

meta{:bash}

:file

Results in pairwise alignment format

*.{aln}

*.sam{:bash}

:file

Results written in sam format

*.{sam}

tsv{:bash}

meta{:bash}

:file

Results in pairwise alignment format

*.{aln}

*.tsv{:bash}

:file

Results in tab-separated output, columns defined by user

*.{tsv}

txt{:bash}

meta{:bash}

:file

Results in pairwise alignment format

*.{aln}

*.txt{:bash}

:file

Tab delimited results in blast-like tabular format

*.{txt}

uc{:bash}

meta{:bash}

:file

Results in pairwise alignment format

*.{aln}

*.uc{:bash}

:file

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

*.{uc}

versions{:bash}

versions.yml{:bash}

: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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