vsearch

Versatile open-source tool for microbiome analysis

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NAME

vsearch \-\-makeudb_usearch — create a UDB database file from a fasta file

SYNOPSIS

vsearch \-\-makeudb_usearch fastafile \-\-output dbfile [options]

DESCRIPTION

The vsearch command --makeudb_usearch creates a UDB database file from the FASTA-formatted sequences in fastafile. The UDB file is a binary format that contains the sequences together with a k-mer index, and can be quickly loaded into memory. Using a UDB file avoids re-indexing the database on every run, which is worthwhile when the same database is searched repeatedly with --usearch_global or --sintax.

Both --makeudb_usearch and --output must be specified.

See vsearch-udb(5) for a description of the UDB file format.

OPTIONS

mandatory options

--makeudb_usearch fastafile
Read fasta sequences from fastafile and create a UDB database. This option is mandatory.

--output filename
Write the UDB database to filename. This option is mandatory.

core options

--dbmask none|dust|soft
Mask regions in the database sequences using the dust method or the soft method, or none to suppress masking. See vsearch-fastx_mask(1) for more details. Warning, when using soft masking, search commands become case sensitive. The default is to mask using dust.

--hardmask
Replace masked nucleotides with Ns.

--wordlength positive integer
Set the length of words (i.e. k-mers) used for sequence indexing and comparisons. Valid values range from 3 to 15. The default is 8.

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.

--maxseqlength positive integer
Discard sequences longer than positive integer (50,000 nucleotides by default).

--minseqlength positive integer
Discard sequences shorter than positive integer (32 nucleotides by default).

--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.

ignored options

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

EXAMPLES

Create a UDB database from a fasta file with default settings:

vsearch \
    --makeudb_usearch db.fasta \
    --output db.udb

Create a UDB database without masking:

vsearch \
    --makeudb_usearch db.fasta \
    --dbmask none \
    --output db.udb

Use the resulting UDB file with --usearch_global:

vsearch \
    --makeudb_usearch db.fasta \
    --output db.udb

vsearch \
    --usearch_global queries.fasta \
    --db db.udb \
    --id 0.97 \
    --blast6out results.b6

SEE ALSO

vsearch-udb2fasta(1), vsearch-udbinfo(1), vsearch-udbstats(1), vsearch-fasta(5), vsearch-udb(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: