Troubleshooting NovaSeq 6000 optical alignment errors, BIRD warnings, and Objective Contamination

See the following for information about and troubleshooting information for onboard optical alignment target errors, BIRD intensity warnings, and objective contamination on the NovaSeq.

The following is the warning given on the NovaSeq: The onboard optical alignment target indicates that maintenance might be required before the next run. The run can continue, but contact Illumina Technical Support for help.

The NovaSeq 6000 intensities are baselined at the BIRD (Built-in Remote Diagnostics) during installation to a specific intensity count for both red and green lasers. The BIRD is the onboard laser target and part of the DAD (Dual Actuation Deck).

Before each run, the NovaSeq Control Software checks the BIRD intensity readings and compares them to the baseline. If the pre-run check falls below 20% from the baseline, this warning is given. This test is used to monitor a decrease in performance due to objective contamination.

Let the run continue as this warning will not have a run performance impact. Contact Illumina Technical Support as an Illumina Engineer visit is required before the next run.

For any feedback or questions regarding this article (Illumina Knowledge Article #1269), contact Illumina Technical Support [e-mail].