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/v0.9.29/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.
DIAMOND is developed by Benjamin Buchfink at the Drost lab, Max Planck Institute for Developmental Biology, Tübingen, Germany.