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

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.

• For low or imbalanced base diversity libraries, Illumina recommends spiking in 10-50% PhiX. It is best to start optimization at a higher percentage of PhiX spike in and reduce over subsequent runs to maximize data output and quality.

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