The bwa-mem story.
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 quality.
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:
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,
Heng
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, either.
Followups:
- Perhaps there is a chance to change something? on Opinionomics by Mick Watson
- An open peer review of BWA-MEM by Aaron Darling.
- Review of bwa mem vy Aaron Darling
Like a war~~
Maybe submitting to the BioRxiv is also a good way: https://www.biorxiv.org/