Thread: BFAST published
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Old 11-20-2009, 04:59 AM   #10
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Originally Posted by Michael.James.Clark View Post
It makes sense to me that they would have higher false positive rates at zero errors because they identify significantly more true positives as well (as 3A is basically gauging true positives and 3B is gauging false positives). My guess is that they are aligning questionable reads that the other aligners are not aligning at all in order to have a higher yield of true positives. I would pose the question of whether one can get BWA and Bowtie to generate fewer false positives, and how that would thereby affect their true positive yield at zero errors. (I have not used them personally, so it's an open question.) Then again, I think it's rather a moot point. The figure is basically demonstrating to me that all of these aligners do quite well at zero-two nucleotide errors.
Both bowtie and bwa are able to find all the occurrences of perfect matches and they always know if a perfect alignment is exact repeat or not. They should not produce false positives in theory. In practice, I evaluated them and they do not, at least not as high as 6%. In addition, I am curious why in 3A aligners do not do equally well for perfect hits. Again, maq and soap guarantee to find all perfect hits.

What I find more striking in that particular figure is how they perform with high error reads, but even more strikingly, reads containing deletions (even deletions of a relatively large size). This is important to me because a lot of studies, particularly whole genome, are searching for novel variants and deletions with relatively low coverage.
I completely agree that Bfast is a great tool for hard reads. The performance of other aligners look reasonable, which implies bfast is very capable. I just think bowtie and bwa should be posed in the right way to avoid confusion.

Last edited by lh3; 11-20-2009 at 05:02 AM.
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