Description

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

Input

Name
Description
Pattern

0 ()

1 ()

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
Description
Pattern

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

Tools

vsearch Documentation

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)

doi: 10.7717/peerj.2584License: GPL v3-or-later OR BSD-2-clause
Authors