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  • MicroHimalaya
    Junior Member
    • Jul 2009
    • 3
    #1

    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!
    Tags: algorithms, bowtie
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