Introducing NovaSeq Control Software version 1.8

NovaSeq Control Software v1.8 can be downloaded from the Illumina software download page and will automatically be queued for download on BaseSpace Sequence Hub.

The software package includes:

• NovaSeq Control Software 1.8.0

• NovaSeq Service Software 1.8.0

• Real Time Analysis 3.4.4

• Universal Copy Service 2.7.2

• Firmware 1.26.10

• Recipes 1.8.0

Prerequisite: NovaSeq Suite installer v1.7.0 or v1.7.5 must have previously been installed on the NovaSeq 6000 before updating to v1.8.0. For any previous versions, first run the v1.7.0 installer before updating to v.1.8.0.

Key improvements from v1.7 to v1.8:

• Line Generation Module (LGM) warm up check is removed from initialization. This results in low occurrence of initialization failures at 93% due to LGM failures and reduced initialization time.

• Enhanced error logging and improved support for Proactive. Added logging of the flow cell (FC) Flatness Pre-run Check results to Proactive.

• Reduced default configuration value "FcFlatnessIndex", mitigating focus/image quality reduction in sequencing runs (changed from 100 µm to 40 µm).

• Improved data copying performance.

• Updated the minimum sequencing temperature from 20°C to 25°C to support sequencing robustness in high humidity. This causes intensity for S2 and S4 runs to be approximately 10-15% lower than prior software versions. No impact in quality metrics.

• Dispense flow rate at specific steps reduced (S4 only) to mitigate the risk of flow cell leaks on the instrument.

• Added two features to help keep waste line from clogging:

  • Backflush with BB3 at the end of cluster generation

  • Bleach flush through the waste lines during post run wash

Key new features:

• Added option to manually check flow cell vacuum pressure prior to run start:

  • “Vacuum check” will check vacuum, FC flatness, and FC Radio-frequency identification (RFID) read

  • Allows flow cells to be tested prior to Xp workflow

• Added ability to enable integration with Illumina Connected Analytics (ICA) in a future cloud release.

• Added options to send the tests performed in Service Software to Proactive upon control software launch.

• Added a check to ensure that the output folder is not in the Run Folder (causes an infinite copy loop).

• Switched to Rclone for file upload. This is the same copy utility used on the NextSeq 1000/2000.

Bug fixes:

• Changed message associated with reagent chiller door being open during sequencing from an error to a warning.

• Fixed a bug where sample sheets of arbitrary names were not automatically converted to the name "SampleSheet.csv" for upload to BaseSpace.

• Fixed a bug where SP flow cells were not read at load flow cell screen.

• Fixed an issue where Universal Copy Service (UCS) would deadlock when deleting a run.

• Fixed an issue where the run may not get marked as complete even though all files were sent to the output location.

• Decreased frequency of run failures caused by imaging timeout.

Note: NovaSeq Control Software v1.8 effects 10x Genomics mkfastq’s (cellranger, cellranger-arc, spacereanger) ability to autocorrect the i5 (index 2) orientation due to a change in Illumina’s reagent name from BP14 to VP14 in the recipe.xml file. For work-arounds to address this issue, visit the 10X Genomics website, select Support, then Q&A, then search for “Will mkfastq be affected by the NovaSeq control software upgrade”.

For any feedback or questions regarding this article (Illumina Knowledge Article #6664), contact Illumina Technical Support [e-mail].