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Last active Nov 23, 2021
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Hi bwa users,
The bwa-mem manuscript has been rejected. Interestingly, the first
reviewer only raised a couple of minor concerns and then accepted the
manuscript in the second round of the review. The second reviewer made
quite a few mistakes on some basic concepts and was hostile from the
beginning. The third reviewer gave fair and good review in the first
round, all of which have been addressed, but he then tried hard to
argue one particular mapper to be the best in accuracy that on the
contrary is inferior to most others in my view. I admit that my
responses were not appropriate, either, when I was in rage under the
charge of being "scientifically dishonest" - because I did not show
that particular mapper in the main figure given its absence of mapping
Anyway, this is the past and you cannot really tell if I am the biased
one when myself is describing the review process. As to the
manuscript, I do not have plan to submit it to another peer-reviewed
journal before I get time from the problems that interest me more. The
manuscript is fairly short and simple. It should not be hard for you
to judge how bwa-mem is compared to those peer-reviewed mappers. If
you decide to use bwa-mem, please cite:
"Li H. (2013) Aligning sequence reads, clone sequences and assembly
contigs with BWA-MEM. arXiv:1303.3997v1 [q-bio.GN]."
I would greatly appreciate. In these years, I sometimes did not pay
enough attention to users' requests and sometimes even lost patience
in answering questions. I deeply apologize for these. Just remember:
when I calm down, I am always grateful to every user, really.
Thank you very much,
PS: I regard this review process as an isolated event. I don't mean to
criticize the journal or the peer-review process in general with this
example. As I said, I was not doing everything in the best way,

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@peterjc peterjc commented May 28, 2013

Thanks Titus - the original source was @lh3's email the bio-bwa-help mailing list, but the SourceForge webpage currently mangles the display:

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