PhiX loading concentrations for validation runs on Illumina sequencing platforms
A PhiX validation run confirms proper hardware and software performance of the instrument. The Illumina PhiX control library is a well-balanced genome with relatively equal representation of A, T, G, and C nucleotides. PhiX lacks an index and is not an appropriate tool for assessing Index Read performance.
It is important that a PhiX control run fall within optimal cluster densities for each platform, as listed in the following table.
\Nondenatured pre-ExAmp concentration \\Patterned flow cells consist of a nanowell with ordered wells, no variation in reported cluster density from run to run \\*\*Final loading concentration
Run length and parameters vary depending on troubleshooting needs, however, Read 1 and 2 must have at least 26 cycles to generate quality scores.
For further information about preparing PhiX for sequencing, see the following documents.
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