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Old 03-11-2010, 06:02 PM   #11
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Location: Québec, Canada

Join Date: Jul 2008
Posts: 260

@bioinfosm The SRA001125 dataset has about 109 X coverage. I think something between 30 and 100 is adequate for Illumina data.

@Mizzou55 You will need paired-end reads. What is your read length? Fragment length? You can handle as much as you can with the available distributed memory. Please note that you need Open-MPI, not MPICH2 or MVAPICH because these libraries are crashing whereas Open-MPI does not. Ray MPI processes always send small messages, and Open-MPI always sends small messages eagerly, but MPICH2-based MPI implementations apparently lack that behavior. For the high heterozygosity, Ray does not support that right now, because Ray currently sees this as non-random error incorporation. I am currently working on color-space for the next upcoming release version 0.0.4, but heterozygosity is the next feature I will add.


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