BLAT

Description

blat website

BLAT is a BLAST-like alignment tool that was originally developed by Jim Kent for the UCSC genome browser. BLAT is extremely fast, but needs to use fasta or 2bit formatted reference databases such as found in see scratch 'fasta' and '2bit' directories. Cite: Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64.

Environment Modules

Run module spider blat to find out what environment modules are available for this application.

Environment Variables

• HPC_KENT_DIR - installation directory
• HPC_KENT_BIN - executable directory

Additional Usage Information

Note

If you encounter segfaults (crashes) while running blat against a larger reference database like nr or md5nr please use a three-way split version of the respective database under /data/reference/fasta and run three blat processes instead of one. The upstream author Jim Kent has been notified of the issue. It's unknown when a fix will be provided.

Categories

genomics