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Diamond is a new high-throughput program for aligning DNA reads or protein sequences against a protein reference database such as NR, at up to 20,000 times the speed of BLAST, with high sensitivity.
See which versions of diamond are available:
$ module avail diamond
Load the diamond environment module and run it:
$ module load diamond/0.9.9 $ diamond
Notes from the sysadmin during installation:
$ cd /tmp $ wget https://github.com/bbuchfink/diamond/releases/download/v0.9.9/diamond-linux64.tar.gz $ tar xf diamond-linux64.tar.gz $ sudo cp diamond diamond_manual.pdf /export/apps/diamond/0.9.9
Diamond requires specially formatted databases, which you create using
diamond makedb subcommand. The input must be a FASTA file, but can be gzip compressed, for example the NR database from NCBI:
$ wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz $ diamond makedb --in nr.gz -d nr $ sudo mkdir -p /export/data/bio/diamond