Alignment Cover for Simulated Illumina Reads

[BertieWooster]

Hello,

I generated 100 M reads using maq’s simulate and simutrain commands. Once I align the reads against an assembly, I note that I get a much higher coverage alignment-wise than if I were to do with the same number of “real” reads. (The simulated reads and the real reads are of the same diploid strain.)

Has anybody gotten similar results?

Thx,
BertieWooster

[zee]

Hi Bertie,

In a simulation with reasonable mutation rates I have always managed to get somewhat better results than with real reads. Error modeling of your real data is always an approximation that will miss events that happen during a real run.
There are other simulators you should try out. One that I like using is the dwgsim program in the DNAA package.