Short Read To Short Read Aligner

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.

alignment

• 2,746 views • link

updated 5.3 years ago by Ram

• written 13.0 years ago by Shaojiang Cai

1 answer

Have a look at Uclust and CD Hit.

• 116 views • link

updated 5.3 years ago by Ram

• written 13.0 years ago by Martin A Hansen

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