Development manual for vsearch 2.32.0, built from the dev branch: it describes changes that are not released yet. The manual for the current release is published separately.

NAME

vsearch --maskfasta — mask low-complexity regions in fasta sequences (deprecated)

SYNOPSIS

vsearch --maskfasta fastxfile --output filename [options]

DESCRIPTION

This command is deprecated. Use --fastx_mask instead (see vsearch-fastx_mask(1)), which can also write fastq output with --fastqout, preserving the quality values of a fastq input. --maskfasta reads fastq too, but writes fasta only.

The vsearch command --maskfasta masks low-complexity regions and simple repeats in the sequences of the fasta- or fastq-formatted fastxfile (quality values are ignored; see vsearch-fasta(5) and vsearch-fastq(5)). The output file is specified with --output, in fasta format.

Masking is controlled with the --qmask option, which accepts three values: dust (default), soft, or none. With dust, low-complexity regions are identified with the DUST algorithm (R. Tatusov and D.J. Lipman, unpublished) and represented as lowercase letters in the output. With soft, lowercase letters in the input are treated as masked and preserved as-is. With none, no masking is applied. Note that with dust and soft masking (the default), the whole sequence is first converted to uppercase, so unmasked regions lose any lowercase they had in the input; with --hardmask, the case of unmasked regions is preserved.

By default, masked regions are written as lowercase letters (soft masking). When --hardmask is specified, masked regions are replaced with N’s instead.

OPTIONS

mandatory options

--output filename
Write to filename, in fasta format.

core options

masking

--hardmask

Replace masked nucleotides with Ns, rather than lowercasing them.

This is also the only masking option that reaches the alignment. Soft and dust masking (see --qmask and --dbmask) only keep masked words out of the k-mer pre-filter that selects candidates; the masked region is still aligned and scored like any other. An N, on the other hand, scores zero and counts as a matching column, so hard masking makes a masked region match whatever it is aligned against, and the reported identity can only go up. Add --n_mismatch to count those columns as mismatches instead.

--qmask none|dust|soft
Mask regions in query sequences using the dust method or the soft method, or none to suppress masking. Values are case-insensitive, so DUST, Dust, and dust are all accepted. See vsearch-fastx_mask(1) for more details. Warning, when using soft masking, search commands become case sensitive: masking excludes masked regions from the k-mer pre-filter that selects candidate targets (the pairwise alignment itself always ignores case). A query with no unmasked stretch of at least the word length samples no k-mers and is therefore compared against every database sequence. The default is to mask using dust.

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 required when compressed data arrives on standard input through a pipe (‘-’), where the format cannot be detected without consuming the stream. It is not needed when reading from a regular file compressed with bzip2, nor when such a file is redirected to standard input: compression is then detected automatically, and a contradicting option is ignored (with a warning when the input is standard input). Pipes other than standard input, such as shell process substitutions and named FIFOs, are always read as uncompressed data; compressed data must arrive on standard input or as a named file.
--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.
--gzip_decompress
Specify that the input pipe is streaming data compressed using Lempel-Ziv coding. See gzip(1) for more details. This option is required when compressed data arrives on standard input through a pipe (‘-’), where the format cannot be detected without consuming the stream. It is not needed when reading from a regular file compressed with gzip, nor when such a file is redirected to standard input: compression is then detected automatically, and a contradicting option is ignored (with a warning when the input is standard input). Pipes other than standard input, such as shell process substitutions and named FIFOs, are always read as uncompressed data; compressed data must arrive on standard input or as a named file.
--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. Messages are written in addition to the standard error, not instead of it; use --quiet to silence the standard error copy (see the --quiet entry for what it spares).
--maxseqlength positive integer
Discard sequences longer than positive integer (50,000 nucleotides by default). The value must not exceed 2,147,481,646 (INT_MAX minus 2,001). When that value is smaller than the effective --minseqlength value (whose default is command-specific), no sequence can pass the length filter: vsearch issues a warning.
--minseqlength non-negative integer
Discard sequences shorter than non-negative integer (1 nucleotide by default). A value of 0 retains empty sequences. When that value is larger than the --maxseqlength value, no sequence can pass the length filter: vsearch issues a warning.
--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. When nothing is left after truncation — an empty string, or one starting with ‘;’ or a blank character — vsearch issues a warning and writes a bare ;sample= annotation.
--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. Existing ;size= annotations are reported unchanged; entries without one receive ;size=1. For this command --sizein is not needed: abundance annotations are always parsed from the input headers.
--threads positive integer
Set the number of computation threads to use, from 1 to 1024. The number of threads should not exceed the number of available CPU cores. The value 0 is also accepted and, like the default, uses all available cores; decimal values are truncated to their integer part. On Linux, “available” accounts for the CPU affinity mask and the cgroup CPU quota of the running process, so a job confined by taskset(1), Slurm, Docker or Kubernetes launches one thread per core it was actually granted, rather than one per core the machine has.
--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

--max_unmasked_pct real
Option is ignored and has no effect.
--min_unmasked_pct real
Option is ignored and has no effect.

EXAMPLES

Mask low-complexity regions in a fasta file using the DUST algorithm (default), and write the results to masked.fasta:

vsearch \
    --maskfasta input.fasta \
    --qmask dust \
    --output masked.fasta

Replace masked regions with N’s instead of lowercase letters (--hardmask):

vsearch \
    --maskfasta input.fasta \
    --hardmask \
    --output masked.fasta

SEE ALSO

vsearch-fastx_mask(1), vsearch-fasta(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.

These manual pages are also published online at https://torognes.github.io/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:

  • 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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