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Old 07-01-2013, 05:24 PM   #8
roshanbernard
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Location: South Korea

Join Date: Feb 2011
Posts: 31
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Quote:
Originally Posted by jonathanjacobs View Post
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
thanks a lot jonathan. Our preference was to save money. we are not interested in gap filling and stuff. we were looking for some specific genes. we have 84 bacterial samples for sequencing. Ur info is helpful. thanks a lot.
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