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MicroHimalaya 07-31-2009 12:38 AM

The Algorithms used in Bowtie.
Recently,I was learning how to use bowtie,but there are a lot of parameters which i don't know how to set. So I study the BWT, FM index ,Suffix Array and so on. When I read this paper:Ultrafast and memory-efficient alignment of short DNA sequences to the human genome,Phased Maq-like search.I don't understand the 3 phases ? Can you help me with it?
Thank you in advanced!

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