NextSeq 1000/2000 Control Software v1.5.0 installation instructions

Please follow all steps below for a successful software (SW) installation.

Note: If version (v) 1.2 or higher version software is currently installed, the user can upgrade to v1.5.0 Control Software directly. If v1.1 software is currently installed, the user must first upgrade to v1.2 software following the instructions found in the v1.2 software release notes.

PREPARATION

These instructions are intended for the v1.5.0 Control Software upgrade only.

1. The total installation time (not including file download times) may take up to 20 minutes.

2. Make sure that you have the password to the ilmnadmin account.

3. To log in to the ilmnadmin account:

   1. If you are already logged in as ilmnuser and in control software, select the control software menu, and then select Exit Application to access the desktop.

   2. Select the power button icon in the upper right corner and log out of ilmnuser.

   3. After you are on the login screen, select ilmnadmin, and then enter the password to log in.

   4. The control software automatically launches once you are logged in.

4. The upgrade installation files require up to 3 GB of free space on your desktop. See file sizes below.

   1. To access your desktop, select the control software menu in the control software, and then select Minimize Application.

   2. Delete or transfer files off the desktop that are not needed.

   3. Empty trash to free space from the drive.

   4. Select Applications, and then Files from the upper left corner of the desktop to launch the file explorer.

   5. On the left panel of the file explorer, right click the Trash icon and select Empty Trash.

5. Launch Chromium to download the software upgrade installers from the Illumina Support Site.

   1. While in desktop view, open the Applications menu on the upper left corner. Select Internet, and then select Chromium.

   2. Note: After launching Chromium, you may receive a prompt to unlock your login keyring. You can safely ignore and cancel out of the prompt.

   3. Use Chromium to browse to the NextSeq 1000 and 2000 Software Downloads page on the Illumina Support Site.

6. Download the following software upgrade installers from the Illumina Support Site and save them to the desktop. Do not extract these files; leave them as .tar.gz.

   1. For offline customers:

   2. v1.5.0 Software (SW) Suite Installer (1 GB)

7. After the files have finished downloading to the desktop, maximize the control software by selecting it from the toolbar.

8. To begin installation, follow the the Offline Installation steps.

ONLINE INSTALLATION

Follow the “Preparation” steps outlined above before continuing.

1. Install SW suite.

   1. Select the software update alert in the control software notification panel and follow the prompts to upgrade the software suite.

   2. When the installation process completes, you will see a message that confirms installation. After closing the prompt, the control software automatically relaunches.

   3. Follow the prompt for the firmware update.

   4. Note: During this process, the screen will go blank. Wait for the image to return and the process to complete.

   5. Follow the prompt to power cycle the instrument.

   6. Note: Make sure to toggle the power switch at the back of the instrument to complete the power cycle after the instrument shuts down.

   7. Power on the instrument and log in as ilmnadmin. The control software automatically launches.

   8. Note: An alert appears indicating that DRAGEN workflows need to be updated. Proceed through the next steps to resolve the alert.

   9. Confirm that the version is updated to v1.5.0 in the About screen in the control software menu.

   10. Proceed to the next step to install DRAGEN workflows.

OFFLINE INSTALLATION

Follow the “Preparation” steps outlined above before continuing.

1. Install SW suite.

   1. Launch control software

   2. Open control software menu.

   3. Select Software Update.

   4. Select Choose… under Browse for Software Update.

   5. Navigate to the desktop and select the installer

   6. Select Update Now.

   7. Follow the password and other prompts.

   8. When the installation process completes, you will see a message that confirms installation. After closing the prompt, the control software automatically relaunches.

   9. Follow the prompt for the firmware update.

   10. Note: During this process, the screen will go blank. Wait for the image to return and the process to complete. If the image does not return after 5 minutes, proceed to the next step to manually toggle the power switch.

   11. Follow the prompt to power cycle the instrument.

   12. Note: Make sure to toggle the power switch at the back of the instrument to complete the power cycle after the instrument shuts down.

   13. Confirm that version is updated in the About screen in the control software menu.

2. Final steps.

   1. After installation completes, delete all the downloaded installation files from the desktop and empty the trash to save space.

   2. Log back into ilmnuser to begin sequencing.

For any feedback or questions regarding this article (Illumina Knowledge Article #7830), contact Illumina Technical Support [e-mail].