Von: Ganga Jeena > If someone can tell me how to do away with this GC bias in reads > or a solution for it. Careful: GC bias is something very different than the GGCxG problem. Regarding the GGCxG problem, the best way to control it is to use in MIRA the proposed end clipping (-CL:pec), though I admit I need to refine it for data >>100x coverage. Regarding a GC bias: that problem should be gone for good since beginning of 2011 at the latest. If you have data from second half of 2009 till 4th quarter 2010, you might have a GC bias and getting rid of that is a pretty daunting task, because it's almost impossible to tell the difference to regular repeats with simple kmer counting algorithms. One would need graph analysis and a lot of other tricks I think. B.