dwgsim illumina mate pairs

[ChrisAU]

Hi there,

I want to simulate Illumina mate pairs and thought of using dwgsim.
However, the manual states that it will create mate pairs, that have --> --> orientation, whereas Illumina mate pairs should have <-- --> orientation.
Am I wrong, or does dwgsim simulate only 454 and Solid mate pairs?

Thanks
Chris

[swNGS]

No, it can do Illumina format Fastas. Remember that with dwgsim you won't get any simulated quality info though

[ChrisAU]

It worked fine for paired-end reads, but not for the mate pairs.
Reverse complementing the first read should do the trick though. For the quality string, I just replaced the default quality string with the values from an average fastqc evaluation.