Description

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

Input

name:type
description
pattern

meta:map

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

queryfasta:file

Query sequences in FASTA format

*.{fasta,fa,fna,faa}

db:file

Reference database file in FASTA or UDB format

*

idcutoff: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: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: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

meta:file

Results in pairwise alignment format

*.{aln}

*.aln:file

Results in pairwise alignment format

*.{aln}

biom

meta:file

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

*.{biom}

*.biom:file

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

*.{biom}

lca

meta:file

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

*.{lca}

*.lca:file

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

*.{lca}

mothur

meta:file

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

*.{mothur}

*.mothur:file

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

*.{mothur}

otu

meta:file

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

*.{otu}

*.otu:file

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

*.{otu}

sam

meta:file

Results written in sam format

*.{sam}

*.sam:file

Results written in sam format

*.{sam}

tsv

meta:file

Results in tab-separated output, columns defined by user

*.{tsv}

*.tsv:file

Results in tab-separated output, columns defined by user

*.{tsv}

txt

meta:file

Tab delimited results in blast-like tabular format

*.{txt}

*.txt:file

Tab delimited results in blast-like tabular format

*.{txt}

uc

meta:file

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

*.{uc}

*.uc:file

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

*.{uc}

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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