text: user1075: 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.
  
  user37: 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.
  
original_text: 1075: <p>I am using BLAT to align two versions of the genome of <em>C. elegans</em>. I can see in the Activity Monitor of my Mac Book Pro High Sierra that <code>blat</code> is using 100% of a CPU. However, is this programme able to use more than one core / CPU to speed up the alignment?</p>
  
  <p>I cannot find such option in the help page of the tool <a href="https://genome.ucsc.edu/goldenPath/help/blatSpec.html" rel="nofollow noreferrer">here</a>.</p>
  
  <p>I installed blat using <code>conda install -c bioconda blat</code>.</p>
  
  <p>I am using the latest version of <code>blat</code>, i.e. 36.</p>
   37: <p>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.</p>
  
  <p>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 <a href="https://github.com/lh3/minimap2/blob/master/cookbook.md#liftover" rel="nofollow noreferrer">minimap2 cookbook</a> gives an example:</p>
  
  <pre class="lang-shell prettyprint-override"><code>minimap2 -cx asm5 --cs ecoli_ref.fa ecoli_canu.fa &gt; ecoli_canu.paf
  echo -e 'tig00000001\t200000\t300000' | paftools.js liftover ecoli_canu.paf -
  </code></pre>
  
  <p>Note that this pipeline is not as mature as UCSC liftOver and is not as scalable.</p>
  