Manual for vsearch 2.32.0, the current release. Changes that are not released yet are described in the development manual.

NAME

vsearch --fastq_chars — analyze fastq files to identify the quality encoding and the range of quality score values used

SYNOPSIS

vsearch --fastq_chars fastqfile [options]

DESCRIPTION

The vsearch command --fastq_chars summarizes the number and composition of sequences and quality strings contained in the input fastq file (see below for an example). Results are written to the standard error stderr(3), and to filename if option --log filename is used.

The command --fastq_chars tries to automatically detect the quality offset (33 or 64) and the fastq format (Solexa, Illumina 1.3+, Illumina 1.5+, Illumina 1.8+, or the original Sanger format) by analyzing the range of observed quality score values. In case of success, --fastq_chars suggests values for the quality offset --fastq_ascii (33 or 64), as well as --fastq_qmin and --fastq_qmax values that could be used with other commands. If the quality encoding is ambiguous, an offset of 33 is favored. For example:

Qmin 45, Qmax 73, Range 29
Guess: -fastq_qmin 12 -fastq_qmax 40 -fastq_ascii 33
Guess: Original Sanger format (phred+33)

A file detected as Solexa is reported as solexa+64, not supported: that format shares the offset 64 with Illumina 1.3+ but defines its scores differently, and vsearch has only the Phred formula (see vsearch-fastq(5)). The suggested --fastq_qmin and --fastq_ascii values will read such a file, but the error probabilities derived from it will be too large at low scores.

For each sequence symbol, --fastq_chars gives the number of occurrences of the symbol, its relative frequency, and the number of consecutive repetitions after the first occurrence in the longest run of that symbol — that is, the longest run length minus one, so a symbol that never appears twice in a row scores 0 (lowercase symbols are converted to uppercase). This matches usearch’s MaxRun column, except that vsearch also counts a run ending with the read. For example:

Letter          N   Freq MaxRun
------ ---------- ------ ------
     A    9050221  25.8%     19
     C    5657659  16.1%      9
     G    8731373  24.9%     11
     T   11610889  33.1%     24

When N symbols are present, their row also reports the range of quality values observed at N positions (Q=min..max).

For each quality symbol, --fastq_chars gives the ASCII value of the symbol (see ascii(7)), its relative frequency, and the number of times a k-mer of that symbol appears at the end of quality strings. The length of the k-mer can be set with the option --fastq_tail (4 by default). For example:

Char  ASCII    Freq       Tails
----  -----  ------  ----------
 '-'     45    0.7%           8
 '.'     46    1.7%           9
 '/'     47    2.8%        2997
 '0'     48    2.4%         221
 '1'     49    0.9%           0
 '2'     50    0.4%           0
 '3'     51    0.4%           0
 '4'     52    0.2%           0
 '5'     53    0.3%           0
 '6'     54    0.0%           0
 '9'     57    1.3%          12
 ':'     58    0.7%           0
 ';'     59    1.3%           1
 '<'     60    0.6%           0
 '='     61    0.2%           0
 '>'     62    0.3%           0
 '?'     63    0.6%           0
 '@'     64    0.3%           0
 'A'     65    1.9%           0
 'B'     66    3.9%          91
 'C'     67    2.2%           0
 'D'     68    1.4%           0
 'E'     69    2.9%           0
 'F'     70   14.7%       24657
 'G'     71   23.5%        5890
 'H'     72   34.5%           9
 'I'     73    0.0%           0

OPTIONS

core options

--fastq_tail positive non-null integer: Count the number of times a series of identical symbols of length k = positive non-null integer, a k-mer, appears at the end of quality strings. By default, k = 4.

secondary options

--bzip2_decompress: Specify that the input pipe is streaming data compressed using Huffman coding. See bzip2(1) for more details. This option is required when compressed data arrives on standard input through a pipe (‘-’), where the format cannot be detected without consuming the stream. It is not needed when reading from a regular file compressed with bzip2, nor when such a file is redirected to standard input: compression is then detected automatically, and a contradicting option is ignored (with a warning when the input is standard input). Pipes other than standard input, such as shell process substitutions and named FIFOs, are always read as uncompressed data; compressed data must arrive on standard input or as a named file.
--gzip_decompress: Specify that the input pipe is streaming data compressed using Lempel-Ziv coding. See gzip(1) for more details. This option is required when compressed data arrives on standard input through a pipe (‘-’), where the format cannot be detected without consuming the stream. It is not needed when reading from a regular file compressed with gzip, nor when such a file is redirected to standard input: compression is then detected automatically, and a contradicting option is ignored (with a warning when the input is standard input). Pipes other than standard input, such as shell process substitutions and named FIFOs, are always read as uncompressed data; compressed data must arrive on standard input or as a named file.
--log filename: Write messages to filename. Messages include program version, start and finish times, elapsed time, amount of memory available, maximum amount of memory consumed, number of cores and command line options, and if need be, command-specific informational messages, warnings, and errors. Messages are written in addition to the standard error, not instead of it; use --quiet to silence the standard error copy (see the --quiet entry for what it spares).; A copy of the statistics computed by --fastq_chars is also recorded.
--no_progress: Suppress the gradually increasing progress indicator normally written to the standard error stderr(3).
--quiet: Suppress messages to the standard output stdout(3) and standard error stderr(3), except for warnings and error messages.

ignored options

--threads positive non-null integer: Command is not multithreaded, option has no effect (a warning is printed when more than one thread is requested).

EXAMPLES

Read from input.fastq.gz, count series of 5 identical symbols at the end of quality strings (--fastq_tail 5), do not write to the standard error (--quiet), and write results to output.log (--log):

vsearch \
    --fastq_chars input.fastq.gz \
    --fastq_tail 5 \
    --quiet \
    --log output.log

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.

These manual pages are also published online at https://torognes.github.io/vsearch/.

COPYRIGHT

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:

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