<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>

CC BY-SA 4.0
2019-01-06T23:19:52.260Z
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?
Biomagician
CC BY-SA 4.0
2019-01-07T10:06:43.993Z
@charlesdarwin LASTZ tool might also be worth a look for this, although it's quite old now...
Chris_Rands
CC BY-SA 4.0
2019-01-06T22:32:02.033Z
2019-01-07T18:28:36.673Z
2019-01-07T18:28:36.673Z
user172818
<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>

<phylogenetics><software-usage><blat>
Can blat use more than one core/CPU to speed up the alignment?
# 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

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## 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 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.

> **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...  

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