@lh3 (Heng Li): you above "I never do simulation with error free reads." Yet you wrote on your webpage that you "simulate error free reads from the diploid genome." That is why I pointed out that you used error-free reads - you said so yourself.
@genericforms: you assert without proof that BWA "clearly wins out" if you account for false positives. Our results contradict this. We simulated both sequencing error (using the ART simulator v1.1.5) and the results of variation between individuals in our experiments, using 3 million paired-end reads. Bowtie2 assigned more reads to their true point of origin than BWA.
We have submitted our results in a paper which is in the peer review process right now. I encourage both of you to do the same. Un-refereed claims on this forum are little more than anecdotes (which is true of my comments too, of course, so I won't be posting any more).
Meanwhile I encourage everyone to try Bowtie2, which in our experiments has demonstrated unparalleled speed, sensitivity, and accuracy.
@genericforms: you assert without proof that BWA "clearly wins out" if you account for false positives. Our results contradict this. We simulated both sequencing error (using the ART simulator v1.1.5) and the results of variation between individuals in our experiments, using 3 million paired-end reads. Bowtie2 assigned more reads to their true point of origin than BWA.
We have submitted our results in a paper which is in the peer review process right now. I encourage both of you to do the same. Un-refereed claims on this forum are little more than anecdotes (which is true of my comments too, of course, so I won't be posting any more).
Meanwhile I encourage everyone to try Bowtie2, which in our experiments has demonstrated unparalleled speed, sensitivity, and accuracy.
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