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 (real)

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 (file)

Results in pairwise alignment format

*.{aln}

biom (file)

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

*.{biom}

lca (file)

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

*.{lca}

mothur (file)

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

*.{mothur}

otu (file)

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

*.{otu}

sam (file)

Results written in sam format

*.{sam}

tsv (file)

Results in tab-separated output, columns defined by user

*.{tsv}

txt (file)

Tab delimited results in blast-like tabular format

*.{txt}

uc (file)

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

*.{uc}

versions (file)

File containing software versions

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