parallelized BLAT
As I had to map assembled reads to the genomic sequence, I used BLAT (the BLAST-like Alignment Tool) for that purpose. BLAT was so fast for landing reads to genomic sequence, but it can be slow if reads are so many. I thought it would be so nice to have multi-threaded BLAT.
And, there is! Just git clone https://github.com/icebert/pblat and then make. pblat binary file will be generated. It works very well with a command like below.
time pblat -threads=4 refgenome.fa query.fa output.psl
-threads=N is only the difference from original BLAT command where N is the number of threads.
An example execution time for execution with N=12 was below.
26353.36s user 88.99s system 798% cpu 55:10.32 total
The license to use this code is same as that of BLAT. Commercial users should take care of this.