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Old 10-07-2010, 06:16 AM   #3
natstreet
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Location: Sweden

Join Date: Nov 2009
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I don't have a good answer but this is something of a hot topic to me as we are doing much the same, although I have higher 454 coverage.

For plants a big factor can be how polymorphic your species is as well as the repeat structure.

In general, I would be really interested to know how people are effectively integrating 454 and Illumina data. Do you compile them on their own and then combine those assemblies or are you compiling the data all together? In either case, what assemblers are you using?
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