vsearch \-\-fastq_chars — analyze fastq files to identify the quality encoding and the range of quality score values used
vsearch \-\-fastq_chars fastqfile [options]
The vsearch command --fastq_chars summarizes the number and
composition of sequences and quality strings contained in the input
fastq file. 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+ or Illumina 1.8+/Sanger) 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)
For each sequence symbol, --fastq_chars gives the number of
occurrences of the symbol, its relative frequency, and the length of the
longest run of that symbol (lowercase symbols are converted to
uppercase). 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
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
--fastq_tail positive non-null integer--bzip2_decompressbzip2(1)). This option is not needed when
reading from a regular file compressed with bzip2.--gzip_decompressgzip(1)). This option is not needed when
reading from a regular file compressed with gzip.--log filename--fastq_chars is also
recorded.--no_progressstderr(3).--quietstdout(3) and standard
error stderr(3), except for warnings and error messages.--threads positive non-null integerRead 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
vsearch-fastq_stats(1),
vsearch-fastq(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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