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Old 07-01-2013, 04:19 AM   #7
jonathanjacobs
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Location: Rockville, MD

Join Date: Apr 2011
Posts: 23
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For what it's worth - higher coverage will NOT not lead to better de novo assemblies. Once you hit about 40-50x , higher coverage may actually produce worse assemblies. Using an Ion318 for a 2MB genome is IMHO a waste of a chip and funding. You would be much better off running a 316 or even a 314 (314's in our lab routinely return 50-60mb of data, more than enough for a 2mb genome) and then using the money you save to outsource a PacBio or Illumina MiSeq run and then do a hybrid assembly.

That's my 2
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