DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data. The key features are:
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This demonstrates a quick example for setting up and using the program on Linux. Installing the software on your system may be done by downloading it in binary format for immediate use:
wget http://github.com/bbuchfink/diamond/releases/download/v2.0.5/diamond-linux64.tar.gz tar xzf diamond-linux64.tar.gz
diamond binary file should be moved to a directory contained in your executable search path (PATH environment variable).
To now run an alignment task, we assume to have a protein database file in FASTA format named
nr.faa and a file of DNA reads that we want to align named
In order to set up a reference database for DIAMOND, the
makedb command needs to be executed with the following command line:
$ diamond makedb --in nr.faa -d nr
This will create a binary DIAMOND database file with the specified name (
nr.dmnd). The alignment task may then be initiated using the
blastx command like this:
$ diamond blastx -d nr -q reads.fna -o matches.m8
The output file here is specified with the
–o option and named
matches.m8. By default, it is generated in BLAST tabular format.
The online documentation is located at http://www.diamondsearch.org. For the markdown source code and an offline, text-based documentation, see: https://github.com/bbuchfink/diamond/tree/master/docs.
DIAMOND is developed by Benjamin Buchfink at the Drost lab, Max Planck Institute for Developmental Biology, Tübingen, Germany.