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Old 06-26-2008, 05:20 PM   #35
green tree
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Location: USA

Join Date: Jun 2008
Posts: 6

Originally Posted by sci_guy View Post

SNP/Indel Discovery
* ssahaSNP - ssahaSNP is a polymorphism detection tool. It detects homozygous SNPs and indels by aligning shotgun reads to the finished genome sequence. Highly repetitive elements are filtered out by ignoring those kmer words with high occurrence numbers. More tuned for ABI SOLiD reads. Developers are Adam Spargo and Zemin Ning from the Sanger Centre. Compaq Alpha, Linux-64, Linux-32, Solaris and Mac
Correct me if I am wrong, but I think that ssahaSNP is more tuned for ABI *Sanger* reads and not ABI SOLiD reads. For shorter reads, you can use ssaha2 (it even has a preconfigured option for Solexa) but you still have the problem of detecting SNPs and indels...

Last edited by green tree; 06-26-2008 at 06:19 PM.
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