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 2 hours ago
charlesdarwin
1,071313
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 2 hours ago
charlesdarwin
1,071313
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 2 hours ago
charlesdarwin
1,071313
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 2 hours ago
charlesdarwin
1,071313
asked 2 hours ago
charlesdarwin
1,071313
asked 2 hours ago
charlesdarwin
1,071313
asked 2 hours ago
charlesdarwin
1,071313
asked 2 hours ago
charlesdarwin
1,071313
1,071313
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.
answered 2 hours ago
user172818♦
4,0171424
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
1 hour ago
@charlesdarwin The eternal theme of bioin-format-ics is format conversion, which is needed here, I am afraid. For simple annotations, you can usepaftools.js liftover.
– user172818♦
57 mins ago
add a comment |
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1 Answer
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1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
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.
answered 2 hours ago
user172818♦
4,0171424
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
1 hour ago
@charlesdarwin The eternal theme of bioin-format-ics is format conversion, which is needed here, I am afraid. For simple annotations, you can usepaftools.js liftover.
– user172818♦
57 mins ago
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.
answered 2 hours ago
user172818♦
4,0171424
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
1 hour ago
@charlesdarwin The eternal theme of bioin-format-ics is format conversion, which is needed here, I am afraid. For simple annotations, you can usepaftools.js liftover.
– user172818♦
57 mins ago
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.
answered 2 hours ago
user172818♦
4,0171424
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.
answered 2 hours ago
user172818♦
4,0171424
answered 2 hours ago
user172818♦
4,0171424
answered 2 hours ago
user172818♦
4,0171424
answered 2 hours ago
user172818♦
4,0171424
4,0171424
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
1 hour ago
@charlesdarwin The eternal theme of bioin-format-ics is format conversion, which is needed here, I am afraid. For simple annotations, you can usepaftools.js liftover.
– user172818♦
57 mins ago
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
1 hour ago
@charlesdarwin The eternal theme of bioin-format-ics is format conversion, which is needed here, I am afraid. For simple annotations, you can usepaftools.js liftover.
– user172818♦
57 mins ago
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
1 hour ago
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
1 hour ago
@charlesdarwin The eternal theme of bioin-format-ics is format conversion, which is needed here, I am afraid. For simple annotations, you can use
paftools.js liftover.– user172818♦
57 mins ago
@charlesdarwin The eternal theme of bioin-format-ics is format conversion, which is needed here, I am afraid. For simple annotations, you can use
paftools.js liftover.– user172818♦
57 mins ago
add a comment |
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