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, C, G, and T 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 in Manual mode. Manual mode allows you to setup the run without using Local Run Manager or BaseSpace™.
NOTE: For the run, set both Index 1 and Index 2 to zero
For more information about preparing PhiX for the NextSeq 500/550 sequencing platform, see the following documents: