vsearch

Versatile open-source tool for microbiome analysis

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NAME

fastq — a text-based format for representing nucleotide sequences and their corresponding quality scores

DESCRIPTION

In fastq files, each entry is made of sequence header starting with a symbol ‘@’, a nucleotidic sequence, a quality header starting with a symbol ‘+’, and a quality string of ASCII characters (offset 33 or 64), each one encoding the quality value of the corresponding position in the nucleotidic sequence.

The sequence header is defined as the string comprised between the initial ‘@’ symbol and the first space, tabulation, or new line symbol, unless the --notrunclabels option is in effect, in which case the entire line is included.

The sequence header should contain printable ASCII characters (33-126). The program will terminate with a fatal error if there are unprintable ASCII characters (see ascii(7)). A warning will be issued if non-ASCII characters (128-255) are encountered.

If the sequence header contains patterns such as [@;]size=integer[;] or [@;]ee=float[;], vsearch can interpret these annotations and use them for chimera detection, clustering, dereplication, filtering and sorting.

The sequence is defined as a string of IUPAC symbols (‘ACGTURYSWKMDBHVN’ and ‘acgturyswkmdbhvn’), starting after the end of the header line and ending before the next header line, or the file’s end. vsearch silently ignores ASCII characters 9 to 13, and exits with an error message if ASCII characters 0 to 8, 14 to 31, ‘.’ or ‘-’ are present. All other ASCII or non-ASCII characters are stripped and complained about in a warning message.

The quality header is defined as the string comprised between the initial ‘+’ symbol and the first space, tabulation, or new line symbol.

The quality string is a string of ASCII characters, starting after the end of the quality header line and ending before the next header line, or the file’s end. The range of valid ASCII characters can extend from ‘!’ to ‘~’ when the offset is 33, and from ‘@’ to ‘~’ when the offset is 64. vsearch silently ignores ASCII characters 9 to 13, and exits with an error message if ASCII characters 0 to 8, 14 to 31, ‘.’ or ‘-’ are present. All other ASCII or non-ASCII characters are stripped and complained about in a warning message.

SEE ALSO

vsearch-fasta(5), vsearch-udb(5)

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: