Short Read To Short Read Aligner

Question

[Shaojiang Cai]

Hi,

I know that BWA, Bowtie, etc can align short reads to the reference genome very efficiently. But can anybody recommend some aligner tailored to align millions of short reads to themselves? I have an application which needs to find similar reads in the library. Thanks.

Answer 1

[Martin A Hansen]

Have a look at Uclust and CD Hit.