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.
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Please read the manual for detailed installation and usage instructions. 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/v0.9.22/diamond-linux64.tar.gz
tar xzf diamond-linux64.tar.gz
The extracted 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 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.
Note:
- The program may use quite a lot of memory and also temporary
disk space. Should the program fail due to running out of either
one, you need to set a lower value for the block size parameter
-b(see the manual). - The default (fast) mode was mainly designed for short reads. For
longer sequences, the sensitive modes (options
--sensitiveor--more-sensitive) are recommended. - The runtime of the program is not linear in the size of the query file and it is much more efficient for large query files (> 1 million sequences) than for smaller ones.
- Low complexity masking is applied to the query and reference sequences by default. Masked residues appear in the output as X.
- The default e-value cutoff of DIAMOND is 0.001 while that of BLAST is 10, so by default the program will search a lot more stringently than BLAST and not report weak hits.
DIAMOND is developed by Benjamin Buchfink at the Detlef Weigel lab, Max Planck Institute for Developmental Biology, Tübingen, Germany.
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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