vsearch

Versatile open-source tool for microbiome analysis

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NAME

vsearch --fastq_eestats2 — report read retention at combinations of length and expected error cutoffs

SYNOPSIS

vsearch --fastq_eestats2 fastqfile --output filename [options]

DESCRIPTION

The vsearch command --fastq_eestats2 analyzes a fastq file and reports the number (and percentage) of sequences that would be retained at each combination of truncation length and maximum expected error threshold. The output is useful for choosing values for --fastq_trunclen and --fastq_maxee when running --fastx_filter (see vsearch-fastx_filter(1)).

The output is a space-aligned table written to --output, preceded by a one-line summary (number of reads, maximum and average length) and a dashed rule. Each row corresponds to a truncation length and each column (after the first) to an EE threshold. Each cell shows the number of reads that would be retained and, in parentheses, the corresponding percentage.

To illustrate with the default cutoffs (--length_cutoffs 50,*,50 and --ee_cutoffs 0.5,1.0,2.0):

Length         MaxEE 0.50         MaxEE 1.00         MaxEE 2.00
------   ----------------   ----------------   ----------------
    50     28595(100.0%)      28595(100.0%)      28595(100.0%)
   100      9854( 34.5%)      15240( 53.3%)      21567( 75.4%)
   150      3022( 10.6%)       6250( 21.9%)      11230( 39.3%)

Rows are always printed for every cutoff length, even when no read reaches it (with zero counts).

The length cutoffs are set with --length_cutoffs (default 50,*,50, meaning 50, 100, 150, …, up to the longest sequence in the file). The EE cutoffs are set with --ee_cutoffs (default 0.5,1.0,2.0).

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). This option is mandatory.

core options

--ee_cutoffs real[,real…]
Set the maximum expected error (EE) thresholds to use as columns in the output table. Requires a comma-separated list of strictly positive floating-point values (e.g., 0.5,1.0,2.0). The default is 0.5,1.0,2.0.

--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.

--fastq_qmax positive 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 41, which is usual for recent Sanger/Illumina 1.8+ files.

--fastq_qmin positive 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 Solexa scores between -5 and 2 used by older formats are thus representable). The default is 0, which is usual for recent Sanger/Illumina 1.8+ files.

--length_cutoffs min,max,increment
Set the range of truncation lengths to use as rows in the output table. Requires three comma-separated integers: the shortest cutoff, the longest cutoff, and the increment between cutoffs. The longest cutoff may be * to use the length of the longest sequence in the input file. The shortest cutoff must be at least 1 and not larger than the longest, the increment must be at least 1, and the list may not contain whitespace. The default is 50,*,50, producing rows at 50, 100, 150, and so on up to the longest sequence.

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 not needed when reading from a regular file compressed with bzip2.

--gzip_decompress
Specify that the input pipe is streaming data compressed using Lempel-Ziv coding. See gzip(1) for more details. This option is not needed when reading from a regular file compressed with gzip.

--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.

--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 with the default cutoffs and write the retention table:

vsearch \
    --fastq_eestats2 input.fastq \
    --output eestats2.tsv

Use custom length and EE cutoffs to focus on shorter reads:

vsearch \
    --fastq_eestats2 input.fastq \
    --length_cutoffs 100,300,50 \
    --ee_cutoffs 0.5,1.0,2.0,3.0 \
    --output eestats2.tsv

SEE ALSO

vsearch-fastq_eestats(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.

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: