vsearch

Versatile open-source tool for microbiome analysis

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NAME

expected error — a quality summary metric for fastq sequences

DESCRIPTION

The expected error (EE) of a fastq read is a single number that summarises the overall quality of that read. It is defined as the sum of the per-base error probabilities across the entire sequence:

EE = P_e(1) + P_e(2) + ... + P_e(L)

where L is the length of the read and P_e(i) is the probability that base i was incorrectly sequenced.

Computing error probabilities from quality scores

Each base quality score Q stored in a fastq file encodes its error probability according to the Phred scale:

P_e = 10^(-Q / 10)

For example:

Q score Error probability Accuracy
Q10 0.1 90%
Q20 0.01 99%
Q30 0.001 99.9%
Q40 0.0001 99.99%

Since error probabilities are always positive, the expected error of a sequence is always greater than zero. It is at most equal to the sequence length, which occurs when every base has an error probability of 1.0.

Why expected error is preferred over average quality

Averaging Phred quality scores directly is mathematically incorrect: quality scores are on a logarithmic scale, while error probabilities are linear. The expected error sums all per-base error probabilities, giving each base equal weight and producing a meaningful global quality estimate.

Poisson interpretation

Because sequencing errors are approximately independent, the expected error can be used as the lambda (λ) parameter of the Poisson distribution to estimate the probability of observing exactly k errors in a read. For a read with EE = 1.0:

vsearch options using expected error

--fastq_maxee real
Discard reads whose total expected error exceeds real. Applied after any trimming step.

--fastq_maxee_rate real
Discard reads whose average expected error per base (EE divided by read length) exceeds real (values from 0.0 to 1.0).

--fastq_truncee real
Truncate reads at the first position where the cumulative expected error would exceed real.

--fastq_truncee_rate real
Truncate reads at the first position where the average expected error per base (cumulative EE divided by current length) would exceed real.

--fastq_eeout / --eeout
Annotate output sequence headers with the expected error value as ;ee=float. Use --xee to remove this annotation from headers.

SEE ALSO

vsearch-fastq(5), vsearch-fastq_eestats(1), vsearch-fastq_eestats2(1), vsearch-fastq_filter(1), vsearch-fastq_mergepairs(1), vsearch-fastx_filter(1)

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) 2014-2026, 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: