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Old 05-13-2011, 11:35 AM   #4
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Location: Boston area

Join Date: Nov 2007
Posts: 747

Obviously if you are doing this in the near future, it's Ion or GSjr, as MiSeq won't be out until the end of year. You could, of course, generate Illumina products & then find a spare lane, but that can be hard to get scheduled.

For this sort of application, GSjr is a more proven system but with a 4X-ish higher cost per run, and if Ion's most recent dataset is to be believed Ion has already passed GSjr on reads/run. So you pay more to get less, but you'll be more confident in that data. Probably for your application you'll be grossly oversampling, so that confidence can be built from very deep data.

At the end of the year, it all depends on if MiSeq comes out on time & on spec and whether Ion can really push the 316 & 318 chips out on time and on spec. The fact you already have a GAIIx might skew things towards MiSeq (since all your libraries will be compatible).
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