A Number of Informative Comments from Heng Li on BWA-MEM Aligner

Heng Li, whose BWA-MEM paper at arxiv may some day become the most cited bioinformatics paper getting rejected by a peer-reviewed journal, wrote a number of informative comments that our readers may find interesting. We are compiling the links here so that you do not miss them.

i) In the commentary “Mapping God Found Scientifically Dishonest by Anonymous Peer Reviewers”, a reader asked -

Would be interesting to know what exactly the concerns of the reviewer were. There are a lot accusations and pretenses, but a lack of facts.

and Heng provided a detailed reply.

ii) On the more technical side, in “Bi-directional BWT and 2BWT Alignment Algorithm”, Heng explained bi-directional bwt algorithm to answer reader Paul’s question.

iii) In a Biostar-related thread, we published Heng’s detailed views on Biostar.

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We also have couple of questions for Heng, if he has time.

i) BLASR paper on aligning Pacbio reads benchmarked the algorithm by comparing with few other aligners, and found BWA-SW to the only one worthy of consideration. Given that BWA-MEM is an improvement over BWA-SW, we wonder how well BWA-MEM would perform on Pacbio reads. Unlike Illumina reads, Pacbio reads are indel-heavy due to technological limitations.

ii) You wrote -

I guess no more than five people in the world understand how bwa-mem finds seeds.

Who are those five people? :)