SOAP2, BWA... which one to choose

[dingxiaofan1]

Hello, everyone. I am new to next generation sequencing data analysis. And I have tried two different methods, SOAP2 and BWA, to assembly my data (Illumina data, targeted region deep sequencing). However, two different programs give two different output. It seems that SOAP2 is more strict than BWA. SOAP2 can map about 70%(including single end read) to the genome, as for BWA, it could map up to more than 90%. Meanwhile, SOAP2 does not allow any small indels as well as many mutations, which is accepted by BWA. So, here is my problem, which one I should choose for further analysis? Which one is more popular and widely acceptable than the other? Thank you.

[epigen]

BWA is the clear favorite around here, competing with Novoalign, see this thread: http://seqanswers.com/forums/showthread.php?t=6822

[dingxiaofan1]

BWA is the clear favorite around here, competing with Novoalign, see this thread: http://seqanswers.com/forums/showthread.php?t=6822

Many thanks. Well, SOAP2 runs extremely fast even on a common desktop computer. The paired-end mapped results of SOAP2 also seems to be right with at most 2 mismatches. So, I am planning to do a quick& conserved alignment by using SOAP2. Then I will take single-end mapped, improperly mapped and unmapped reads as input to do a second realignment through BWA. And then repeat the procedure by novoalign. The total process will cost, I guess, very limit time, since the first alignment is very quick and input for others has been reduced greatly.