Development manual for vsearch 2.32.0, built from the dev branch: it describes changes that are not released yet. The manual for the current release is published separately.

NAME

vsearch --fastq_eestats — report per-position quality and expected error statistics

SYNOPSIS

vsearch --fastq_eestats fastqfile --output filename [options]

DESCRIPTION

The vsearch command --fastq_eestats analyzes a fastq file and reports per-position statistics on quality scores, per-base error probabilities, and cumulative expected errors. The output is a 21-column tab-separated table written to --output, with one row per read position. The columns are:

  • Pos: position in the reads (1-based).
  • Recs: number of reads extending to or past this position.
  • PctRecs: percentage of reads reaching this position.
  • Min_Q, Low_Q, Med_Q, Mean_Q, Hi_Q, Max_Q: distribution of the Phred quality score at this position (minimum, lower quartile, median, mean, upper quartile, maximum).
  • Min_Pe, Low_Pe, Med_Pe, Mean_Pe, Hi_Pe, Max_Pe: distribution of the per-base error probability at this position.
  • Min_EE, Low_EE, Med_EE, Mean_EE, Hi_EE, Max_EE: distribution of the cumulative expected errors accumulated from position 1 to this position.

The quality encoding and accepted score range can be set with --fastq_ascii, --fastq_qmin, and --fastq_qmax.

See vsearch-expected_error(7) for a description of the expected error metric.

OPTIONS

mandatory options

--output filename
Write the statistics table to filename (tab-separated for --fastq_eestats, space-aligned for --fastq_eestats2).

core options

--fastq_ascii 33|64
Specify the offset used as the basis for the fastq quality score when reading fastq files. For example, an offset of 33 means that a quality value of 41 is represented by the 74th ASCII symbol (33 + 41 = 74), which is ‘J’. See ascii(7) for a view of the ASCII character set. The offset value is either 33 or 64, default is 33.

The offset matters even to a command that never decodes a quality score: it is what the reader compares the observed quality symbols against before warning that the file may use the other encoding, it sets the default of --fastq_qmax (the highest score the offset can represent), and the sum rules on --fastq_qmin and --fastq_qmax are stated in terms of it.

--fastq_qmax integer
Specify the maximal quality score accepted when reading fastq sequences. Stop with an error message if a quality score higher than the specified value is read. The offset (see --fastq_ascii) plus the maximal score may not exceed 126, the last printable ASCII character: scores up to 93 with offset 33, up to 62 with offset 64. The default is the highest score the offset can represent (93 with offset 33, 62 with offset 64), so no quality score is rejected unless this option is lowered. Before version 2.32.0 the default was 41, the usual maximum for Sanger/Illumina 1.8+ files, which rejected PacBio HiFi and nanopore files outright.
--fastq_qmin integer
Specify the minimal quality score accepted when reading fastq sequences. Stop with an error message if a quality score lower than the specified value is read. The offset (see --fastq_ascii) plus the minimal score must be at least 33, the first printable ASCII character: scores down to 0 with offset 33, down to -31 with offset 64. The value may therefore be negative, which is what the negative scores of older formats require, but note that those formats are not supported (see vsearch-fastq(5)). The default is 0, which is usual for recent Sanger/Illumina 1.8+ files.

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).
--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

Analyze a fastq file and write per-position statistics to a file:

vsearch \
    --fastq_eestats input.fastq \
    --output eestats.tsv

Specify a Phred+64 quality encoding and write results quietly:

vsearch \
    --fastq_eestats input.fastq \
    --fastq_ascii 64 \
    --quiet \
    --output eestats.tsv

SEE ALSO

vsearch-fastq_eestats2(1), vsearch-fastq_stats(1), vsearch-fastx_filter(1), vsearch-fastq(5), vsearch-expected_error(7)

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

Copyright (C) 2014-2026, 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.
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