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[internship project] condition where BLAST > BWA.

I've asked my student to write a program to convert BLAST/XML to BAM and to compare the results (quality, not speed) with BWA .

For now, the results are quite similar :-) ( testing with viral genomes , nanopore data,... )

Do you know any dataset (in SRA ...) or condition where Blast could outperform Bwa ?

Thanks.

P.

blast bwa
• 2,433 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

Blast is in theory more sensitive to highly divergent hits IF you use the right parameters.

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updated by Ram Ram • written by lh3 lh3

2 answers

Are you referring to NGS applications only?

  • Maybe for PacBio reads: high error rates, and long few sequences.
  • to detect contaminants or partial sequences
  • I'd sometimes use only the unmapped portion of reads and blast against NT (how long does the internship last, to give enough time to blast millions of reads?)
  • anything meta-genomics, especially viral metagenomics, sometimes done using blastx against viral proteins
  • once we have assembled contigs
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updated by Ram Ram • written by Michael Dondrup Michael Dondrup

Are you referring to NGS applications only?

Currently, yes.

  1. PacBio: Yes, nice idea.
  2. contaminants: Yes but I would need some FASTQS known to be contaminated.
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updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

Cross-species (or more distantly-related) mapping should favor BLAST. Human to mouse, for example.

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updated by Ram Ram • written by Brian Bushnell Brian Bushnell

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