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BLAST: Difference between revisions
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Blast search can greatly benefit from data parallelism by splitting the query file into multiples queries and running these queries against the database. | Blast search can greatly benefit from data parallelism by splitting the query file into multiples queries and running these queries against the database. | ||
==== Preprocess ==== | ==== Preprocess ==== <!--T:16--> | ||
In order to accelerate the search, the <tt>seq.fa</tt> file must be split into smaller chunks. The file chunks should be at least <tt>1Mb</tt> or greater, but not '''smaller''' as it may hurt the parallel file system. | In order to accelerate the search, the <tt>seq.fa</tt> file must be split into smaller chunks. The file chunks should be at least <tt>1Mb</tt> or greater, but not '''smaller''' as it may hurt the parallel file system. | ||
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}} | }} | ||
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Note: the <tt>zcat</tt> utility could be used here to read a gzip compressed FASTA file and pass its decompressed content to GNU Parallel. | Note: the <tt>zcat</tt> utility could be used here to read a gzip compressed FASTA file and pass its decompressed content to GNU Parallel. | ||