How to set up a PhiX validation run on the NextSeq 500/550 in manual mode
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.
Open the NextSeq 500/550 Control Software (NCS).
Select Experiment.
Select Sequence.
Select Manual.
Note: For the run, set both Index 1 and Index 2 to zero.
Configure the output folder (refer to How to connect benchtop instruments and Local Run Manager to a network location).
Follow the prompts on the screen to load the flow cell.
Follow the prompts on the screen to discard spent reagents, reload the spent reagents tray, and load a new buffer cartridge.
Load the reagent cartridge.
Review the run configuration.
Next, perform the instrument self-check, after which the PhiX validation run begins sequencing.
For more information about preparing PhiX for the NextSeq 500/550 sequencing platform, see the following documents:
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