parallelized blat

blat with multi-threads support

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.

pblat can run on Linux and Mac OS.

Install

To compile the source code, simply enter the source code directory in terminal and issue the "make" command. When the compiling finished, the executable pblat will locate in the same directory. Then it can be moved to where you want.

Run

To run with multiple threads, add option "-threads=<number of threads>" in the command line.

Licence

pblat is modified from blat, the licence is the same as blat. The source code and executables are freely available for academic, nonprofit and personal use. Commercial licensing information is available on the Kent Informatics website.

Cite

Wang M & Kong L. pblat: a multithread blat algorithm speeding up aligning sequences to genomes. BMC Bioinformatics 2019, 20(1). [full text]

Docker

docker run -u $(id -u):$(id -g) -v $(pwd):/data icebert/pblat -threads=4 <database.fa> <query.fa> <out.psl>

Copyright (C) 2012 - 2020 Wang Meng

Contact me: [email protected]