vsearch

NAME

vsearch — a versatile open-source tool for metabarcoding and metagenomics

SYNOPSIS

vsearch <command> [file] [options]

(see below for a list of available commands)

WARNING: this is a pre-release of the future revised and updated vsearch documentation. Users can already refer to this content for the commands listed below, but be aware that most vsearch commands are not yet featured.

DESCRIPTION

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, pairwise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metabarcoding, metagenomics, genomics, and population genetics.

VSEARCH COMMANDS

Each command is described in a dedicated manpage. For example, type man vsearch-fasta2fastq to read about the --fasta2fastq command. Manpages reffering to commands all belong to section 1 (executable programs). Some vsearch manpages belong to section 5 (file formats and conventions). For example, type man 5 vsearch-fastq or man 'vsearch-fastq(5)' to read about the fastq format as-seen by vsearch.

FASTA/FASTQ/SFF file processing:

• vsearch-fasta2fastq(1)
  Convert a fasta file to a fastq file with fake quality scores.
• vsearch-fastq_chars(1)
  Analyze fastq files to identify the quality encoding and the range of quality score values used.
• vsearch-fastq_stats(1)
  Analyze fastq files and output detailed statistics: read length distribution, quality score distribution, length vs quality distribution, effect of expected error and length filtering, effect of quality score and length filtering.

FILE FORMATS

• vsearch-fasta(5)
  Specify the fasta format, as used by vsearch.
• vsearch-fastq(5)
  Specify the fastq format, as used by vsearch.

(also SFF, and UDB).

SEE ALSO

swarm, swipe, usearch

CITATION

Rognes T, Flouri T, Nichols B, Quince C, Mahé F. (2016) VSEARCH: a versatile open source tool for metagenomics. PeerJ 4:e2584 doi: 10.7717/peerj.2584

REPORTING BUGS

Submit suggestions and bug-reports at https://github.com/torognes/vsearch/issues, send a pull request on https://github.com/torognes/vsearch, or compose a friendly or curmudgeont e-mail to Torbjørn Rognes (torognes@ifi.uio.no).

AVAILABILITY

Source code and binaries are available at https://github.com/torognes/vsearch.

COPYRIGHT

Copyright (C) 2014-2024, Torbjørn Rognes, Frédéric Mahé and Tomás Flouri

All rights reserved.

Contact: Torbjørn Rognes torognes@ifi.uio.no, Department of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316 Oslo, Norway

This software is dual-licensed and available under a choice of one of two licenses, either under the terms of the GNU General Public License version 3 or the BSD 2-Clause License.

GNU General Public License version 3

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

The BSD 2-Clause License

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

ACKNOWLEDGMENTS

We would like to thank the authors of the following projects for making their source code available:

• vsearch includes code from Google’s CityHash project by Geoff Pike and Jyrki Alakuijala, providing some excellent hash functions available under a MIT license.
• vsearch includes code derived from Tatusov and Lipman’s DUST program that is in the public domain.
• vsearch includes public domain code written by Alexander Peslyak for the MD5 message digest algorithm.
• vsearch includes public domain code written by Steve Reid and others for the SHA1 message digest algorithm.
• vsearch binaries may include code from the zlib library, copyright Jean-Loup Gailly and Mark Adler.
• vsearch binaries may include code from the bzip2 library, copyright Julian R. Seward.

VERSION HISTORY

(inject history here)

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