How to perform system checks on the NovaSeq 6000

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

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

• System checks will be 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 System. Required consumables:

1. An S3 wash flow cell or S4 flow cell per side (a 4-lane flow cell is needed for all tests).

2. SBS wash cartridges and Cluster wash trays are needed for the Impedance test only.

3. Used buffer cartridges from previous runs (NovaSeq Control Software (NVCS) will check 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 (sometimes, it will have enough BB3 buffer leftover from the previous run and will not need additional DI water added).

Before starting System Check: * After Power Cycle, to launch NovaSeq Service Software (NVSS):

• Close NovaSeq Control Software (NVCS).

• Open NovaSeq Service Software (found on the desktop).

• Wait for 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, PE (Paired-End) 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 or S4 flow cell and select the flow cell type from the drop-down menu.* Starting a system check with an incorrect flow cell type will give a "Wash flow cell required" error message.

4. Return Home.

5. Select System Check from Home Screen.* All tests are pre-selected.

• Results will be pass/fail or NaN.

• Select "Start" to run tests.

1. The View Report option at the end of the system check will show 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].