[Bio-bwa-help] BWA-MEM

[Fatih T. <ftu...@gm...>]

Dear all,

I have been looking for some documentation about BWA-MEM algorithm which,
according to manual page, does not have an official publication yet. Is
there any document that explains/shows the details about it? For instance,
what are the things common between MEM and BWA-SW (and BWA backtrack) in
terms of the steps followed (as explained in Li&Durbin '9 and '10)?

I got this info from BWA's SF page :
The BWA-MEM algorithm is based on an algorithm finding super-maximal exact
matches (SMEMs), which was first published with the fermi assembler paper
in 2012. I first implemented the basic SMEM algorithm in the fastmap
command for an experiment and then extended the basic algorithm and added
the extension part in Feburary 2013 to make BWA-MEM a fully featured mapper.

Thanks a lot in advance.

--
Fatih