BLAT

A low-memory footprint genetic sequence alignment tool

Homepage Version(s): 34

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BLAT requires an environment module

In order to use BLAT, you must first load the appropriate environment module:

module load gnu

BLAT is one of the bioinformatics tools available on RCC systems. It is a genetic sequence alignment tool that is somewhat similar to the BLAST alignment tool. BLAT is designed to assemble and index entire genomes and is designed to look for sequences with very high similarity.

Using BLAT on the HPC

To run BLAT, type the following commands into the command line:

$ module load gnu
$ blat -OPTIONS DBFILE QUERYFILE OUTPUTFILE

Replace the -OPTIONS argument with the list of options required for your job, and the DBFILE, QUERYFILE, and OUTPUTFILE arguments with the names of your own files. A list of options is available by simply typing blat into the command line.