NovaSeq Software Release Notes

Introduction

These Software Release Notes detail new features, improvements, and known issues for the NovaSeq™ 6000 Sequencing System for improved sequencing robustness.

For more information on the NovaSeq 6000, see the NovaSeq 6000 Sequencing System Guide (document # 1000000019358) available on the NovaSeq 6000 Sequencing System support pages.

The software package includes:

• NovaSeq Control Software 1.8.2
• NovaSeq Service Software 1.8.0
• Real Time Analysis 3.4.4
• Universal Copy Service (UCS) 2.7.3
• Firmware 1.26.10
• Recipes 1.8.0

I. NovaSeq Control Software 1.8.2

New Features:

• None

Improvements:

• None

Fixed Issues:

• Fixed issue of run failure due to loss of BaseSpace cloud connection.
  • If Instrument Performance Data (IPD) is selected: IPD will be removed from the sequencing settings and allow the sequencing run to proceed.
  • If Illumina cloud run monitoring and storage or run monitoring only is selected: the pre-run check will fail and display a notification to retry the pre-run check or return to the BaseSpace login screen.

Known Issues:

• In rare occurrences, the reagent chiller door sensor warning during Pre-Run Checks may prevent continuation for both flow cell sides (instead of only the failed side) during a dual flow cell run. User is required to exit the workflow and setup runs for both sides again.
• 10X Genomics users: Demultiplexing using mkfastq (cellranger, cellranger-arc, cellranger-atac, or spaceranger) can cause reads to be assigned to the Undermined FASTQ files.
• 10X Genomics has released a workaround available on their Knowledge Base.

II. NovaSeq Service Software 1.8.0

New Features:

• None

Improvements:

• None

Bug Fixes:

• None

III. Real Time Analysis 3.4.4

New Features:

• None

Improvements:

• None

Bug Fixes:

• None

IV. Universal Copy Service 2.7.3

New Features:

• None

Improvements:

• None

Bug Fixes:

• None

V. Firmware 1.26.10

New Features:

• None

Improvements:

• None

Bug Fixes:

• None

VI. Recipes 1.8.0

New Features:

• None

Improvements:

• None

Bug Fixes:

• None

VII. Manual Install Notes

NOTE: If v1.8 or higher version software is currently installed, the user can upgrade to v1.8.2 Control Software directly. If v1.7 or lower version is currently installed, the user must first upgrade to v1.8 software following the instructions found in the v1.8 software release notes.

• Before upgrading, check the Recipe Fragment Version currently installed within the NovaSeq Control Software About screen.

• Description of the "About" screen:

  The "About" screen shows details for NovaSeq Control Software Version 1.8.2, including Instrument (NovaSeq 6000), Instrument Serial Number (A00288R), Computer Name (NVSQ-A00288), Recipe Fragment Version (1.8.0), and Total Run Count (539). It also provides contact information for Customer Service and Technical Support, along with the Illumina website. A "Done" button is visible.

• The 1.8.2 System Suite Installer will install the 1.8.0 Recipe Fragment version.
• Please contact Illumina tech support techsupport@illumina.com to schedule an FSE visit to restore Recipe Fragment Version 1.8.1 if previously installed.
• No action needed if previously using Recipe Fragment Version 1.8.0.
• Prior to performing a manual software upgrade, power cycle the instrument and ensure the following:
  • The system is powered 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, then download the installer from the Illumina Support Site and unzip to C:\Program Files\Illumina.
• Run the NovaSeq Software Suite Installer.
  • Confirm time on system matches local time.
  • If prompted, ensure firewall settings allow network communication for NVCS (see below).

• Description of the "Windows Security Alert" dialog for NVCS:

  A "Windows Security Alert" dialog box indicates that "Windows Defender Firewall has blocked some features of this app". It specifies the app name, publisher (Microsoft Corporation), and path. Checkboxes allow the user to permit communication on "Domain networks", "Private networks", and "Public networks". "Allow access" and "Cancel" buttons are present.

• Reboot system as prompted by NovaSeq Software Suite Installer.
• On first-time launch of NovaSeq Control Software 1.8, navigate to Settings, update any options as necessary, and click Save.
  • If prompted, ensure firewall settings allow network communication for UCS (see below).

• Description of the "Windows Security Alert" dialog for UCS:

  A "Windows Security Alert" dialog box indicates that "Windows Defender Firewall has blocked some features of universal-copy-service". It specifies the app name, publisher (Illumina), and path. Checkboxes allow the user to permit communication on "Domain networks", "Private networks", and "Public networks". "Allow access" and "Cancel" buttons are present.

Known Issues

• A manual power cycle is required to complete the installation if the “Restart” button on the “Setup Successful” screen does not function.
• Login screen appears blank or continually loads on first-time launch of NovaSeq Control Software 1.8 when Settings have not been saved once after update.
  • If seen, please follow these steps:
    • Navigate to Settings.
    • Switch to a different Hosting Region (e.g. switch to CAC1, then back to USE1).
    • Deselect BaseSpace Sequence Hub, hit save, then reselect BaseSpace Sequence Hub, hit save.
    • Attempt to set up run with BSSH Login.
  • If the issue is not resolved, please call technical support for next steps.
• On rare occasions, the installer can fail to communicate with one of the devices on the system in the required time and the software update process will not complete.
  • If seen, please power cycle and run the installer package again.
  • If the issue persists, please call technical support for next steps.
  • If encountering this issue via BSSH download, please call technical support for next steps.
• On rare occasions, UCS or Rclone processes may persist in the background and cause install to fail.
  • If seen, please follow these steps:
    • Power cycle.
    • Navigate to C:\ProgramData\Illumina\Universal Copy Service and move the Runs and Logs folder to another location to ensure that the Universal Copy Service folder is empty.
    • Run the installer package again.
  • If the issue persists, please call technical support for next steps.

Release History