parallelized blat with multi-threads support

Download .zip Download .tar.gz View on GitHub

Welcome to pblat

This program is for single computer with multiple core processors. For cluster version of pblat, please refer to pblat-cluster .

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.


To compile the source code, simply enter the source code directory in terminal and issue the make command.

$ make

or you can install with bioconda.


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

$ pblat -threads=<int> [other options] <database.fasta> <query.fasta> <out.psl>


$ docker run -u $(id -u):$(id -g) -v $(pwd):/data icebert/pblat -threads=<int> [other options] <database.fasta> <query.fasta> <out.psl>


pblat is modified from blat, the license 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.


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


Copyright (C) 2012 - 2020 Wang Meng

Contact me: wangm@mail.cbi.pku.edu.cn