HPC:BLAT
From HPC wiki
BLAT
UCSC's BLAT is installed across all HPC nodes.
Usage
BLAT can be loaded as a module:
[asrini@node061 ~]$ module load blat-v3
[asrini@node061 ~]$ blat
blat - Standalone BLAT v. 35 fast sequence search command line tool
usage:
blat database query [-ooc=11.ooc] output.psl
where:
database and query are each either a .fa , .nib or .2bit file,
or a list these files one file name per line.
-ooc=11.ooc tells the program to load over-occurring 11-mers from
and external file. This will increase the speed
by a factor of 40 in many cases, but is not required
output.psl is where to put the output.
Subranges of nib and .2bit files may specified using the syntax:
/path/file.nib:seqid:start-end
or
/path/file.2bit:seqid:start-end
or
/path/file.nib:start-end
With the second form, a sequence id of file:start-end will be used.
