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Old 09-13-2010, 01:29 PM   #1
BertieWooster
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Location: Sydney, Australia

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Default Alignment Cover for Simulated Illumina Reads

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
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Old 09-13-2010, 08:15 PM   #2
zee
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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.
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