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Old 09-20-2016, 03:23 AM   #3
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Join Date: Feb 2008
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Both are sequencers by function. Considering their sequence outputs, you can decide which is appropriate for the application you intend to use them for and the number of samples you need to multiplex.

NextSeq uses 2-color chemistry as opposed to HiSeq 4000 (which uses standard Illumina type) so that may be one consideration. HiSeq 4000 requires libraries of more exacting specifications (in terms of insert size etc) that would be one more consideration.
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