Hi- As the post title says: When and why one should prefer bwa aln over bwa mem?
The bwa docs say that bwa mem is preferable for longer reads ( > 70 bp). But what is the disadvantage of using bwa mem for shorter reads?
Part of the reason I'm asking is that I have a variety of libraries of read lengths from ~40-70 bp to 150 bp, after quality and adapter trimming, mostly paired-end. I'd rather use one tool for all the read lengths to keep things consistent and bwa mem seems the best choice, unless there is some good reason to avoid it for reads between ~40 and 70 bp.
I have the impression (not tested) that bwa mem is much slower than bwa aln on shorter reads, but that's not an issue for me.