Adquate tool for mapping to a short reference

Question

[vimartin]

Hi,

I have to repetitively perform an alignment task of reads to short (few hundreds bp) references. I intended to use bwa mem but I'm wondering if there is any tool which is more suited for this task, I only found a discussion (http://seqanswers.com/forums/showthread.php?t=9900) on this subject from 2011 which, I guess, is now outdated.

Would you have any idea of efficient tools to use or should I stick with bwa mem?

Thanks.

Answer 1

[Istvan Albert]

The answer depends on what you need to find. Short read aligners are optimized to report the best and closest matches. Won't even look for more distant alignments. In return they operate at very high speeds. There are generic aligners like lastz that are slower but report more distant alignments.

[vimartin]

Hi,

Thanks for your answer. In fact I'm more concerned about speed, and I was wondering whether I some other tools could be faster than classic aligners?