slackbuilds/academic/diamond/README

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