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. Below are instructions for setting up a PhiX validation run for the NextSeq™ 500/550 system using Prep tab available through BaseSpace Hub. BaseSpace Prep Tab is not available on NextSeq instruments running NextSeq Control Software v4.0 or higher. Follow instructions in the Local Run Manager: How to set up a PhiX validation run support bulletin to set up a PhiX validation run in NextSeq Control Software v4 or higher.
For more information about BaseSpace Hub Prep tab and preparing PhiX for the NextSeq 500/550 system, see the following documents: