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DIAMOND is a sequence aligner for protein and translated DNA searches,
designed for high performance analysis of big sequence data. The key
features are:
- Pairwise alignment of proteins and translated DNA at 500x-20,000x
speed of BLAST.
- Frameshift alignments for long read analysis.
- Low resource requirements and suitable for running on standard
desktops or laptops.
- Various output formats, including BLAST pairwise, tabular and XML,
as well as taxonomic classification.
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 `reads.fna`.
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.
Publication:
Buchfink B, Xie C, Huson DH, "Fast and sensitive protein alignment using
DIAMOND", Nature Methods 12, 59-60 (2015). doi:10.1038/nmeth.3176
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