vsearch

NAME

vsearch \-\-fasta2fastq — convert a fasta file to a fastq file with fake quality scores

SYNOPSIS

vsearch \-\-fasta2fastq fastafile \-\-fastqout fastqfile [options]

DESCRIPTION

The vsearch command --fasta2fastq converts fasta sequences into fastq sequences by adding fake quality scores. See vsearch-fasta(5) and vsearch-fastq(5) for more information on these formats. Sequences are written to the file specified with --fastqout. The quality score can be adjusted with the --fastq_qmaxout option (default is 41). The quality offset can be adjusted with the --fastq_asciiout option (either 33 or 64, default is 33).

OPTIONS

mandatory options

--fastqout filename
Write sequences to filename in fastq format, with fake quality scores. The default quality value (41) and offset (33) can be changed with options --fastq_qmaxout and --fastq_asciiout.

core options

--fastq_asciiout 33|64
Specify the offset used as the basis for the fastq quality score when writing fastq output 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_qmaxout positive integer
Specify the fake quality score used when writing the fastq file. The default is 41, which is the usual maximal quality score for recent Sanger/Illumina 1.8+ files (maximal quality score was 40 in older formats). Accepted values range from 0 to 93 when the quality offset is set to 33 (see --fastq_asciiout), and from 0 to 62 when the quality offset is set to 64.

secondary options

--bzip2_decompress
Specify that the input pipe is streaming data compressed using Huffman coding (see bzip2(1)). 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)). This option is not needed when reading from a regular file compressed with gzip.
--label_suffix string
Add the suffix string to sequence headers when writing fasta or fastq files. For example, with --label_suffix ";status=healthy", sequence header ‘>seq1’ becomes ‘>seq1;status=healthy’.
--lengthout
Add a sequence length annotation (;length=integer) to each sequence header when writing fasta or fastq files.
--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.
--relabel string
Replace sequence headers with the prefix string and a ticker (1, 2, 3, etc.). For example, with --relabel "cluster:", the first sequence header becomes ‘>cluster:1’, the second sequence header becomes ‘>cluster:2’, and so on. To retain annotations, use their corresponding options (--lengthout, --eeout, and --sizeout). Use --relabel_keep to retain old sequence identifiers.
--relabel_keep
Retain old sequence identifiers by including them at the end of the new headers, after a space.
--relabel_md5
Replace each sequence header with the MD5 digest derived from the sequence itself. The sequence is converted to upper case, and each ‘U’ is replaced with a ‘T’ before computation of the digest. The MD5 digest is a 128-bit value, represented using a string of 32 ASCII characters. Each pair of characters encodes an hexadecimal value, ranging from x00 to xff. See md5(3) for more details on MD5, and --relabel_sha1 for an alternative algorithm. To retain annotations, use their corresponding options (--lengthout, --eeout, and --sizeout). Use --relabel_keep to retain old sequence identifiers.
--relabel_self
Replace each sequence header with the sequence itself. To retain annotations, use their corresponding options (--lengthout, --eeout, and --sizeout). Use --relabel_keep to retain old sequence identifiers.
--relabel_sha1
Replace each sequence header with the SHA1 digest derived from the sequence itself. The sequence is converted to upper case, and each ‘U’ is replaced with a ‘T’ before computation of the digest. The SHA1 digest is a 160-bit value, represented using a string of 40 ASCII characters. Each pair of characters encodes an hexadecimal value, ranging from x00 to xff. See sha1(3) for more details on SHA1, and --relabel_md5 for an alternative algorithm. To retain annotations, use their corresponding options (--lengthout, --eeout, and --sizeout). Use --relabel_keep to retain old sequence identifiers.
--sample string
Add the the given sample identifier string to sequence headers when writing fasta or fastq files. For instance, if string is ‘ABC’, the text ;sample=ABC will be added to the headers. Note that string will be truncated at the first ‘;’ or blank character. Other characters (alphabetical, numerical and punctuations) are accepted.
--sizein
Use the abundance annotations present in sequence headers when reading fasta or fastq file. Search for the pattern [>@;]size=integer[;]. Entries without abundance annotations are silently assumed to be of size=1.
--sizeout
Add abundance annotations to sequence headers when writing fasta or fastq files. Add the pattern ;size=integer;. If option --sizein is not used, abundance values are set to 1 for all entries. If --sizein is used, existing abundance annotations are simply reported to output files.
--xee
Strip expected error (ee) annotations from sequence headers when writing fasta or fastq files. Search for the pattern [>@;]ee=float[;]. Expected error annotations are added by the synonymous options --fastq_eeout and --eeout described in vsearch-fastx_filter(1).
--xlength
Strip sequence length annotations from sequence headers when writing fasta or fastq files. Search for the pattern [>@;]length=integer[;]. Sequence length annotations are added by the --lengthout option.
--xsize
Strip abundance annotations from sequence headers when writing fasta or fastq files. Search for the pattern [>@;]size=integer[;]. Abundance annotations are added by the --sizeout option.

ignored options

--threads positive non-null integer
Command is not multithreaded, option has no effect.

EXAMPLES

Convert sequences in input.fasta into fastq sequences, with fake quality values (Q = 40), and a quality offset of 64. Add sequence length annotations (--lengthout). Write the results to output.fastq:

vsearch \
    --fasta2fastq input.fasta \
    --fastq_qmaxout 40 \
    --fastq_asciiout 64 \
    --lengthout \
    --fastqout output.fastq

For instance, the following fasta input:

>s1
CACCGCGGTTATACGAGGGGCTCAAATTGATATT
>s2
CACCGCGGTTATACGAGGGGCTCAAATTGATATT
AATATCAATTTGAGCCCCTCGTATAACCGCGGTG

becomes:

@s1;length=34
CACCGCGGTTATACGAGGGGCTCAAATTGATATT
+
hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
@s2;length=68
CACCGCGGTTATACGAGGGGCTCAAATTGATATTAATATCAATTTGAGCCCCTCGTATAACCGCGGTG
+
hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh

(note that fastq output files are not wrapped)

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

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.

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