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1- Format database:\\
<code>
diamond  makedb --in <your_database_as_fasta_file> -d <output_file_prefix>
</code>
   * This will create a file with extension dmnd.\\
\\
2- Run diamond:\\
<code>
diamond blastp --threads 8 -d <database> -q <query_file> -a <output_file> --salltitles --max-target-seqs 2000 --evalue 0.00001 --more-sensitive
</code>
   * Name the output file with the extension daa (DIAMOND alignment archive).\\
\\
3- View results:\\
<code>
diamond view -o <output_file> -f tab -a <infile>
</code>
   * <infile> here is the DIAMOND alignment archive file created at step 2.\\
   * Name the output file with the extension tsv.\\
   * Alternatively, you can specify the information to list in the tabular output like this:\\
<code>
diamond view -o <output_file> -f "6 qseqid sseqid pident length mismatch gapopen qstart qend qlen sstart send slen evalue" -a <infile>\\
</code>
   * I like to have the lengths of the query and subject sequences (qlen and slen respectively) which is not included in the default tabular format.\\
\\
Steps 2 and 3 can be gathered in the same shell script. For example:\\
<code>
#!/bin/bash
#$ -S /bin/bash
. /etc/profile
#$ -o diamond_nr.out
#$ -e diamond_nr.err
#$ -cwd
#$ -pe threaded 8
diamond blastp --threads 8 -d <database> -q <query_file> -a <output_file> --salltitles --max-target-seqs 2000 --evalue 0.00001 --more-sensitive
diamond view -o <output_file> -f tab -a <infile>
</code>
For help:\\
<code>
diamond --help
</code>

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