2.9 years ago by
University Park, USA
I have had very good experiences with BWA-mem and frankly I would be surprised to hear that it were noticeably slower than Bowtie 2 - although I have not measured it myself.
In my work I have noticed that BWA-mem, when used with default alignment parameters, performs a far more sensitive search than Bowtie 2 - hence it might run slower especially when benchmarked with data of nearly identical reads where the sensitivity of the search is less relevant. One can tune Bowtie 2 to produce the results with the same sensitivity but then the invocation looks like this and runtimes are substantially slower:
bowtie2 -D 20 -R 3 -N 1 -L 20 -i S,1,0.50
just to be able to produce the same quality alignments as BWA-mem. For this reason I pretty much prefer to use BWA-mem.