When the query file format is fasta, you can specify many threads to process it. It can reduce run time linearly, and use almost equal memory as the original blat program. This is useful when you blat a big query file to a huge reference like human whole genome sequence.
The program is based on the original blat program which was written by Jim Kent.
Check which versions are available:
$ module avail pblat
Load one version into your environment and run it:
$ module load pblat/2.1 $ pblat
Note: To run with multiple threads, add option "-threads=<number of threads>" in the command line. Make sure to match the number of threads with the number requested in your SLURM SBATCH job parameters.
Notes from the sysadmin during installation:
$ cd /tmp $ wget https://github.com/icebert/pblat/archive/2.1.tar.gz $ cd pblat-2.1 $ make $ sudo mkdir -p /export/apps/pblat/2.1/bin $ sudo cp pblat /export/apps/pblat/2.1/bin