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My lab has just gotten access to start running our samples on a NovaSeq. Previously, they have been running all their WGS on a HiSeq. Our primary concern is will we run into issues running the same sample on a NovaSeq, when all the previous data has been generated using a HiSeq. The goal of the study is structural variant detection. I've asked some of the other BX people around here and they don't really know, so I'm wondering if anyone here has looked at comparisons between NovaSeq and HiSeq. My gut instinct is that it should not matter too much, but I'm not intimate with the NovaSeq quite yet.
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