Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-01-06T23:19:52.260Z
Answers.Text: 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?
Answers.UserDisplayName: Biomagician
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-01-07T10:06:43.993Z
Answers.Text: @charlesdarwin LASTZ tool might also be worth a look for this, although it's quite old now...
Answers.UserDisplayName: Chris_Rands
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-01-06T22:32:02.033Z
Answers.LastActivityDate: 2019-01-07T18:28:36.673Z
Answers.LastEditDate: 2019-01-07T18:28:36.673Z
Answers.UserDisplayName: user172818
Body: <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>
  
Tags: <phylogenetics><software-usage><blat>
Title: Can blat use more than one core/CPU to speed up the alignment?
ThreadText: # Can blat use more than one core/CPU to speed up the alignment?
  
  (Asked by: username_0 on 2019-01-06)
  
  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](https://genome.ucsc.edu/goldenPath/help/blatSpec.html).
  
  I installed blat using `conda install -c bioconda blat`.
  
  I am using the latest version of `blat`, i.e. 36.
  
  **Tags:** phylogenetics, software-usage, blat
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-01-06. Score: 6 | Accepted answer
  
  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](https://github.com/lh3/minimap2/blob/master/cookbook.md#liftover) gives an example:
  
  ```shell
  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.
  
  > **Comments:**
  > **username_0**: 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?  
  > **username_2**: @charlesdarwin LASTZ tool might also be worth a look for this, although it's quite old now...  
  
  ---
  
  