I am using BLAT to align two versions of the genome of C. elegans. I can see in the Activity Monitor of my Mac Book Pro High Sierra that blat is using 100% of a CPU. However, is this programme able to use more than one core / CPU to speed up the alignment?

I cannot find such option in the help page of the tool here.

I installed blat using conda install -c bioconda blat.

I am using the latest version of blat, i.e. 36.


1 Answer 1


BLAT can only use one CPU. It is actually not the right tool for full-genome alignment. For "two versions" of the same species, MUMmer and minimap2 are orders of magnitude faster and probably give better alignment.

EDIT (moving comment to answer): OP comments that the purpose of this alignment is for lifting over annotations using the UCSC PSL-based pipeline. So far there are no converters for minimap2's SAM/PAF or MUMmer's delta formats. With the UCSC pipeline, you have to write a converter by yourself. An alternative approach is to use minimap2's liftover. The minimap2 cookbook gives an example:

minimap2 -cx asm5 --cs ecoli_ref.fa ecoli_canu.fa > ecoli_canu.paf
echo -e 'tig00000001\t200000\t300000' | paftools.js liftover ecoli_canu.paf -

Note that this pipeline is not as mature as UCSC liftOver and is not as scalable.

  • $\begingroup$ I need an alignment in PSL format for downstream tools needed for lifting over an annotation. Do you know if I can get an alignment in psl format with nucmer or minimap2? $\endgroup$ Jan 6, 2019 at 23:19
  • 1
    $\begingroup$ @charlesdarwin LASTZ tool might also be worth a look for this, although it's quite old now... $\endgroup$ Jan 7, 2019 at 10:06

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