Best practices when updating to NovaSeq 6000 Control Software v1.8

This bulletin outlines best practices when updating to NovaSeq 6000 Control Software (NVCS) v1.8 and how to prepare for the first run after the update. Newer NovaSeq 6000 instruments need firewall adjustments before and after the update. Check the firewall settings before starting the update, after the software has been updated, and after the power cycle is complete.

Before performing a manual software update, power cycle the instrument and verify the following:

• The system is turned on.

• The system is not currently performing a sequencing run or system wash.

• The system is not currently uploading sequencing run data.

• Log in using a Windows administrator account on the NovaSeq 6000, then download the installer from the Illumina Support Site and unzip to C:\Program Files\Illumina.

Confirm Firewall settings

1. Search for ‘Allow an App through Windows Firewall’ in the Windows search bar.

2. Select Change Settings at the top right corner of the window.

3. Confirm that the three boxes for Domain, Public, and Private are checked for the following apps.

• Instrument Shell (all instances)

• Universal-copy-service (does not appear until after the software is launched the first time, refer to additional instructions below)

• Illumina.Voyagersimulator

• Windows Host Process (RundII32)

Note: The following Apps may or may not be present, please check Domain, Public, and Private for all instances you may see.

• Illumina - Rabbit MQ (TCP-in)

• Illumina - Rabbit MQ (UDP-in)

• Illumina - VM Ping (ICMP-in)

• Allow NTP

• Block Microsoft RPC/135

• Block Microsoft RPC/49666

• Block SSH/22

Note: Upon initialization of the NovaSeq Control Software after the update, make sure to check all three boxes (domain, private, and public) for universal-copy-service Windows Defender Firewall prompt (pictured below). In some cases, by default, the prompt only has one of the three boxes checked. Check all three boxes and select Allow access to proceed.

Best practices after the software update

This section outlines a best practice before the first run after the update. Following these steps will decease delays during run setup of the first run after the update.

Reselect BaseSpace Settings for runs uploaded to BaseSpace:

1. From the Main Menu of the NVCS, select Settings.

2. Uncheck and check the BaseSpace Sequence Hub checkbox.

3. Select the Hosting Location drop-down menu and select the correct location. For users in the United States, select USA (N. Virginia). This step must be performed even if the server has been previously selected.

4. Select Save.

For any feedback or questions regarding this article (Illumina Knowledge Article #7441), contact Illumina Technical Support [e-mail].