A PhiX validation run confirms proper hardware and software performance of the instrument. The Illumina PhiX control library is derived from the small, well characterized bacteriophage PhiX genome and is a well-balanced library 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. Below are instructions for setting up the sample sheet for a PhiX validation run for the MiSeq system using Illumina Experiment Manager (IEM) v1.15.
Run length and parameters vary depending on troubleshooting needs and reagent chemistry version. The recommended minimal read length is 26 cycles for Read 1 and Read 2 if using a MiSeq v2 50 cycle kit.
For more information about Illumina Experiment Manager and preparing PhiX for the MiSeq sequencing platform, see the following documents: