Can blat use more than one core/CPU to speed up the alignment?
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.
alignment sequence-alignment software-usage blat
asked Jan 6 at 22:02
charlesdarwincharlesdarwin
1,098313
add a comment |
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.
alignment sequence-alignment software-usage blat
asked Jan 6 at 22:02
charlesdarwincharlesdarwin
1,098313
add a comment |
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.
alignment sequence-alignment software-usage blat
asked Jan 6 at 22:02
charlesdarwincharlesdarwin
1,098313
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.
alignment sequence-alignment software-usage blat
alignment sequence-alignment software-usage blat
asked Jan 6 at 22:02
charlesdarwincharlesdarwin
1,098313
asked Jan 6 at 22:02
charlesdarwincharlesdarwin
1,098313
asked Jan 6 at 22:02
charlesdarwincharlesdarwin
1,098313
asked Jan 6 at 22:02
charlesdarwincharlesdarwin
1,098313
asked Jan 6 at 22:02
charlesdarwincharlesdarwin
1,098313
1,098313
add a comment |
add a comment |
1 Answer
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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 'tig00000001t200000t300000' | paftools.js liftover ecoli_canu.paf -
Note that this pipeline is not as mature as UCSC liftOver and is not as scalable.
answered Jan 6 at 22:32
user172818♦user172818
4,0821424
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?
– charlesdarwin
Jan 6 at 23:19
1
@charlesdarwin LASTZ tool might also be worth a look for this, although it's quite old now...
– Chris_Rands
Jan 7 at 10:06
add a comment |
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1 Answer
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1 Answer
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active
oldest
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votes
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 'tig00000001t200000t300000' | paftools.js liftover ecoli_canu.paf -
Note that this pipeline is not as mature as UCSC liftOver and is not as scalable.
answered Jan 6 at 22:32
user172818♦user172818
4,0821424
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?
– charlesdarwin
Jan 6 at 23:19
1
@charlesdarwin LASTZ tool might also be worth a look for this, although it's quite old now...
– Chris_Rands
Jan 7 at 10:06
add a comment |
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 'tig00000001t200000t300000' | paftools.js liftover ecoli_canu.paf -
Note that this pipeline is not as mature as UCSC liftOver and is not as scalable.
answered Jan 6 at 22:32
user172818♦user172818
4,0821424
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?
– charlesdarwin
Jan 6 at 23:19
1
@charlesdarwin LASTZ tool might also be worth a look for this, although it's quite old now...
– Chris_Rands
Jan 7 at 10:06
add a comment |
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 'tig00000001t200000t300000' | paftools.js liftover ecoli_canu.paf -
Note that this pipeline is not as mature as UCSC liftOver and is not as scalable.
answered Jan 6 at 22:32
user172818♦user172818
4,0821424
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 'tig00000001t200000t300000' | paftools.js liftover ecoli_canu.paf -
Note that this pipeline is not as mature as UCSC liftOver and is not as scalable.
answered Jan 6 at 22:32
user172818♦user172818
4,0821424
edited Jan 7 at 18:28
answered Jan 6 at 22:32
user172818♦user172818
4,0821424
answered Jan 6 at 22:32
user172818♦user172818
4,0821424
answered Jan 6 at 22:32
user172818♦user172818
4,0821424
4,0821424
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?
– charlesdarwin
Jan 6 at 23:19
1
@charlesdarwin LASTZ tool might also be worth a look for this, although it's quite old now...
– Chris_Rands
Jan 7 at 10:06
add a comment |
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?
– charlesdarwin
Jan 6 at 23:19
1
@charlesdarwin LASTZ tool might also be worth a look for this, although it's quite old now...
– Chris_Rands
Jan 7 at 10:06
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?
– charlesdarwin
Jan 6 at 23:19
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?
– charlesdarwin
Jan 6 at 23:19
1
1
@charlesdarwin LASTZ tool might also be worth a look for this, although it's quite old now...
– Chris_Rands
Jan 7 at 10:06
@charlesdarwin LASTZ tool might also be worth a look for this, although it's quite old now...
– Chris_Rands
Jan 7 at 10:06
add a comment |
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