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!
Thank you in advanced!