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

Join Date: Jul 2009
Posts: 14
Default Alignment Cover for Simulated Illumina Reads


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?

BertieWooster is offline   Reply With Quote
Old 09-13-2010, 08:15 PM   #2
NGS specialist
Location: Malaysia

Join Date: Apr 2008
Posts: 249

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.
zee is offline   Reply With Quote

align cover, maq

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