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