Originally posted by robp
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As an unrelated side-note, Illumina's NextSeq systems - in my testing - give vastly inferior output compared to HiSeq or MiSeq (and the data was certified by Illumina as being in-spec). I believe this may largely be due to the software; improved base-calling software may be able to substantially improve the output of NextSeq, or other new platforms. That said, for a market-dominant company to release a new product that is undeniably inferior to prior products, indicates to me that sequencing companies have good reason to support alternatives, if they desire better data.
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