vsearch

Versatile open-source tool for microbiome analysis

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NAME

vsearch \-\-fastx_getsubseq — extract a subsequence from a fasta or fastq file by label

SYNOPSIS

vsearch \-\-fastx_getsubseq fastxfile (\-\-fastaout | \-\-fastqout | \-\-notmatched | \-\-notmatchedfq) filename \-\-label string [\-\-subseq_start position] [\-\-subseq_end position] [options]

DESCRIPTION

The vsearch command --fastx_getsubseq extracts a subsequence region from a sequence in a fasta or fastq file whose header matches the label given with --label. The input format is detected automatically (see vsearch-fasta(5) and vsearch-fastq(5)).

This command is similar to --fastx_getseq (see vsearch-fastx_getseq(1)), but instead of writing the full matching sequence, it writes only the region specified by --subseq_start and --subseq_end. Positions are 1-based: the first base is at position 1. By default, extraction starts at position 1 and ends at the last position of the sequence.

Label matching follows the same rules as --fastx_getseq: the label must match the entire header by default (after truncation at the first space or tab — use --notrunclabels to disable truncation). Use --label_substr_match to allow matching anywhere in the header. Matching is not case-sensitive.

Matching sequences (trimmed to the requested region) are written to --fastaout and/or --fastqout. Non-matching sequences are written in full to --notmatched and/or --notmatchedfq.

Input (2 sequences):  --label "seq1" --subseq_start 3 --subseq_end 6:

>seq1                 extracted (--fastaout):   not matched (--notmatched):
ACGTACGT      -->     >seq1  GTAC              >seq2  TTTTTTTT
>seq2
TTTTTTTT

OPTIONS

mandatory options

--label is required. At least one of --fastaout, --fastqout, --notmatched, or --notmatchedfq must be specified.

core options

--label string
Specify the sequence label to match. Unless --label_substr_match is given, the label must match the entire header. The comparison is not case-sensitive. Headers are truncated at the first space or tab character unless --notrunclabels is used.

--label_substr_match
Allow the label specified with --label or --labels to match anywhere in the header. Without this option, the label must match the entire header.

--subseq_start positive integer
Start position of the subsequence to extract. Positions are 1-based (the first base is position 1). Default is 1 (start of the sequence).

--subseq_end positive integer
End position of the subsequence to extract. Positions are 1-based (the first base is position 1). Default is the last position of the sequence.

--fastaout filename
Write the extracted subsequences to filename, in fasta format.

--fastqout filename
Write the extracted subsequences to filename, in fastq format (see vsearch-fastq(5)). Requires fastq input.

--notmatched filename
Write the sequences that were not extracted to filename, in fasta format.

--notmatchedfq filename
Write the sequences that were not extracted to filename, in fastq format. Requires fastq input.

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.

--fasta_width positive integer
Set the maximal width of sequences when writing fasta files. Longer sequences are folded and written on several lines. Default width is 80 nucleotides. Set to zero (0) to suppress folding.

--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. Accepted values range from 0 to 93 if the offset is 33 (see --fastq_ascii), or range from 0 to 62 if the offset is 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. Accepted values range from 0 to 93 if the offset is 33 (see --fastq_ascii), or range from 0 to 62 if the offset is 64. The default is 0, which is usual for recent Sanger/Illumina 1.8+ files. Older formats may use scores between -5 and 2.

--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.

--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).

--notrunclabels
Retain whole sequence headers in output files. By default, vsearch truncates sequence headers at first space or tabulation. This option suppresses truncation.

--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 also 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 (16 bytes), 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, and --relabel_sha1 for an alternative hashing algorithm. To retain annotations, use their corresponding options (--lengthout, --eeout, and --sizeout). Use --relabel_keep to also 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 also 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 (20 bytes), 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, and --relabel_md5 for an alternative hashing algorithm. To retain annotations, use their corresponding options (--lengthout, --eeout, and --sizeout). Use --relabel_keep to also retain old sequence identifiers.

--sample string
Add 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. string is silently truncated at the first ‘;’ or whitespace character (space, tab, newline, carriage return, vertical tab or form feed), so such characters should not be used in string. 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

Extract bases 21 to 270 from a target sequence, discarding the rest:

vsearch \
    --fastx_getsubseq input.fasta \
    --label "target_seq" \
    --subseq_start 21 \
    --subseq_end 270 \
    --fastaout region.fasta

Extract from position 100 to the end of the sequence in a fastq file:

vsearch \
    --fastx_getsubseq input.fastq \
    --label "read1" \
    --subseq_start 100 \
    --fastqout tail.fastq \
    --notmatchedfq unmatched.fastq

SEE ALSO

vsearch-fastx_getseq(1), vsearch-fastx_getseqs(1), vsearch-fasta(5), vsearch-fastq(5)

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: