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Old 08-18-2010, 09:14 AM   #22
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Location: Boston

Join Date: Feb 2008
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Originally Posted by aleferna View Post
@Heng Li

Well I don't care too much about SNPs, actually what I work with resembles more chip-seq technology. All I need to know is the position, not the alignment. I like BWA because I need to work with both 454 and HiSeq, and compare them, so I prefer BWA because seems to be able to manage both. Does Ssaha2 manage high throughput?
Ssaha2 is designed for high throughput sequencing. As I said, it is usually faster than blat, although less easy to use, I would say.
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