fasta — a text-based format for representing nucleotide sequences
In fasta files, each entry is made of a header and a sequence. The
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 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.
When using the option --sizein, if the header matches the patterns
>[;]size=integer;identifier, >identifier;size=integer;identifier, or
>identifier;size=integer[;], vsearch will interpret integer as the
number of occurrences (or abundance) of the sequence in the study. That
abundance information is used or created during chimera detection,
clustering, dereplication, sorting and searching.
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.
vsearch-fastq(5),
vsearch-udb(5)
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
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).
Source code and binaries are available at https://github.com/torognes/vsearch.
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
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