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diamond_blast [2017/09/11 06:01] – 129.173.94.20diamond_blast [2017/09/11 06:12] (current) – 129.173.94.20
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 +**A quick guide to Diamond by Tommy Harding**\\
 +\\
 1- Format database:\\ 1- Format database:\\
 <code> <code>
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 2- Run diamond:\\ 2- Run diamond:\\
 <code> <code>
-diamond blastp --threads 8 -d <database> -q <query_file> -a <output_file> --salltitles --max-target-seqs 2000 --evalue 0.00001 --more-sensitive+diamond blastp --threads 8 -d <database> -q <query_file> -a <output_file_as_DIAMOND_alignment_archive> --salltitles --max-target-seqs 2000 --evalue 0.00001 --more-sensitive
 </code> </code>
    * Name the output file with the extension daa (DIAMOND alignment archive).\\    * Name the output file with the extension daa (DIAMOND alignment archive).\\
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    * Alternatively, you can specify the information to list in the tabular output like this:\\    * Alternatively, you can specify the information to list in the tabular output like this:\\
 <code> <code>
-diamond view -o <output_file> -f "6 qseqid sseqid pident length mismatch gapopen qstart qend qlen sstart send slen evalue" -a <infile>+diamond view -o <output_file> -f 6 qseqid sseqid pident length mismatch gapopen qstart qend qlen sstart send slen evalue -a <infile>
 </code> </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.\\    * 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.\\
diamond_blast.1505120513.txt.gz · Last modified: by 129.173.94.20