DIAMOND 2016

Introduction

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 100x-10,000x 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.¹

Installed version(s)

The following versions are installed and currently available...

... on environment hpc-env/8.3:

• name/version-GCC-8.3.0
• DIAMOND/2.0.9-GCCcore-8.3.0
• DIAMOND/2.0.9-GCC-8.3.0

Loading / Using DIAMOND

To load the desired version of the module, use the module load command, e.g.

module load hpc-env/8.3
module load DIAMOND 

Always remember: this command is case sensitive!

After loading the module, you can get more information on how to use diamon with the command diamond help which prints out detailled output. The very basic part of said output is as follows:

$diamond help

diamond v2.0.9.147 (C) Max Planck Society for the Advancement of Science
Documentation, support and updates available at http://www.diamondsearch.org
Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)



Syntax: diamond COMMAND [OPTIONS]



Commands:
makedb Build DIAMOND database from a FASTA file
blastp Align amino acid query sequences against a protein reference database
blastx Align DNA query sequences against a protein reference database
view View DIAMOND alignment archive (DAA) formatted file
help Produce help message
version Display version information
getseq Retrieve sequences from a DIAMOND database file
dbinfo Print information about a DIAMOND database file
test Run regression tests
makeidx Make database index



General options:
--threads (-p) number of CPU threads
--db (-d) database file
--out (-o) output file
--outfmt (-f) output format


Documentation

For more information you can look up the projects github wiki page.