mirror of
https://github.com/Ponce/slackbuilds
synced 2024-11-07 20:27:02 +01:00
33 lines
1.3 KiB
Text
33 lines
1.3 KiB
Text
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
|