Can blat use more than one core/CPU to speed up the alignment?












2














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







share|improve this question



























    2














    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







    share|improve this question

























      2












      2








      2







      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







      share|improve this question













      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






      share|improve this question













      share|improve this question











      share|improve this question




      share|improve this question










      asked yesterday









      charlesdarwincharlesdarwin

      1,078313




      1,078313






















          1 Answer
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          active

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          5














          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.






          share|improve this answer























          • 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
            yesterday






          • 1




            @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. EDIT: on paftools liftover see here.
            – user172818♦
            yesterday








          • 1




            @charlesdarwin LASTZ tool might also be worth a look for this, although it's quite old now...
            – Chris_Rands
            22 hours ago











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          1 Answer
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          1 Answer
          1






          active

          oldest

          votes









          active

          oldest

          votes






          active

          oldest

          votes









          5














          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.






          share|improve this answer























          • 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
            yesterday






          • 1




            @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. EDIT: on paftools liftover see here.
            – user172818♦
            yesterday








          • 1




            @charlesdarwin LASTZ tool might also be worth a look for this, although it's quite old now...
            – Chris_Rands
            22 hours ago
















          5














          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.






          share|improve this answer























          • 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
            yesterday






          • 1




            @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. EDIT: on paftools liftover see here.
            – user172818♦
            yesterday








          • 1




            @charlesdarwin LASTZ tool might also be worth a look for this, although it's quite old now...
            – Chris_Rands
            22 hours ago














          5












          5








          5






          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.






          share|improve this 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 'tig00000001t200000t300000' | paftools.js liftover ecoli_canu.paf -


          Note that this pipeline is not as mature as UCSC liftOver and is not as scalable.







          share|improve this answer














          share|improve this answer



          share|improve this answer








          edited 13 hours ago

























          answered yesterday









          user172818♦user172818

          4,0621424




          4,0621424












          • 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
            yesterday






          • 1




            @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. EDIT: on paftools liftover see here.
            – user172818♦
            yesterday








          • 1




            @charlesdarwin LASTZ tool might also be worth a look for this, although it's quite old now...
            – Chris_Rands
            22 hours 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
            yesterday






          • 1




            @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. EDIT: on paftools liftover see here.
            – user172818♦
            yesterday








          • 1




            @charlesdarwin LASTZ tool might also be worth a look for this, although it's quite old now...
            – Chris_Rands
            22 hours 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
          yesterday




          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
          yesterday




          1




          1




          @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. EDIT: on paftools liftover see here.
          – user172818♦
          yesterday






          @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. EDIT: on paftools liftover see here.
          – user172818♦
          yesterday






          1




          1




          @charlesdarwin LASTZ tool might also be worth a look for this, although it's quite old now...
          – Chris_Rands
          22 hours ago




          @charlesdarwin LASTZ tool might also be worth a look for this, although it's quite old now...
          – Chris_Rands
          22 hours ago


















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