How to perform system checks on the NovaSeq 6000

Note: The NovaSeq 6000 system checks should only be performed when requested by Illumina Tech Support and must be carried out under guidance.

• Power cycle the instrument before performing the system check.*

• System checks are performed on both sides of the instrument.

• System checks take ~2 hours to complete all tests.

*For further information, see the Knowledge Base article How to Power Cycle the NovaSeq 6000

Required consumables:

1. An S3 Wash Flow Cell or used S4 Flow Cell per side (a 4-lane flow cell is required for all tests).

2. SBS Wash Cartridges and Cluster Wash Trays are required for the Impedance Test only.

3. Used Buffer Cartridges from previous runs (NovaSeq 6000 Control Software (NVCS) checks for the RFID). The wash buffer cartridge will not work.

   • Add 200 ml of deionized (DI) water or BB3 reagent (wash buffer) in position VB2 of the used buffer cartridge (there may be sufficient BB3 buffer volume left from the previous run and no additional DI water is needed).

   

Before starting System Check:

• After the power cycle, to launch the NovaSeq Service Software (NVSS):

  • Close the NovaSeq Control Software (NVCS).

  • Open the NovaSeq Service Software (launch icon on the desktop).

  • Wait for the Service Software to initialize on the instrument.

• To select the system check save location or to select a different default output folder location for System Check results:

  • Select Menu, then select Output Repository.

    • The default is C:.

  • If needed, change locations only for .csv and .xml reports.

  • Select Save.

  

To Start a System Check:

1. Load the SBS Wash Cartridge, Paired-End (PE) Cluster Wash Cartridge, and a used Buffer Cartridge (add 200 ml DI water in the buffer cartridge if needed, as described above).

2. Select Load Flow Cell from the Home screen.

3. Load an S3 Wash Flow Cell or used S4 Flow Cell and select the flow cell type from the drop-down menu.

• Note: starting a system check with an incorrect flow cell type will give a "Wash flow cell required" error message.

1. Return Home.

2. Select System Check from Home Screen.

• All tests are pre-selected.

• Select Start to run tests.

• Results will be "Pass", "Fail" or "NaN".

1. The View Report option at the end of the system check shows the output folder for the check results.

2. Share the results folder with Illumina Technical Support ([e-mail]).

For further information, see the Knowledge Base article How to Perform a System Health Check on the NovaSeq 6000 Video

For any feedback or questions regarding this article (Illumina Knowledge Article #2495), contact Illumina Technical Support [e-mail].