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