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


Name (Type)

meta (map)

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

queryfasta (file)

Query sequences in FASTA format


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


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.


Name (Type)

aln (file)

Results in pairwise alignment format


biom (file)

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


lca (file)

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


mothur (file)

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


otu (file)

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


sam (file)

Results written in sam format


tsv (file)

Results in tab-separated output, columns defined by user


txt (file)

Tab delimited results in blast-like tabular format


uc (file)

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


versions (file)

File containing software versions



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)