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Which controls should be used when sequencing low diversity libraries on a MiSeq?

Illumina recommends adding PhiX at 1% to all sequencing runs as an internal control.
For low-diversity libraries, spike in higher percentages of phiX to add base diversity to the run. The percentage of PhiX to depends on the diversity of the library, and requires optimization. * Monotemplates may require 30% PhiX.
  • Real Time Analysis (RTA) v1.17.28 or later requires a minimum of 5% PhiX spike-in for low-diversity libraries, when using MiSeq v3 reagents for sequencing.
  • MiSeq v2 runs require higher phiX spike in than MiSeq v3 runs.
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