When can runs be staggered on NovaSeq 6000?

On the NovaSeq 6000, a run can be set up and started on the idle side of the instrument while a run is in progress on the other side. This is referred to as a staggered start.

Staggered runs are set up at specific times during the run on the other side, as indicated by the following start countdown timer states, which are displayed on the instrument.

1. Run Start: Available

• Staggered start is available.

• The date and time show when staggered start will become available.

• Select Sequence to start a new staggered run after the current cycle is complete.

2. Run Start: Unavailable

• Staggered start is unavailable.

• The date and time show when staggered start will be available on the other side of the instrument.

3. Waiting...

• If a new run is attempted when staggered start is unavailable, the state changes to Waiting... and the date and time show the approximate time that the instrument will be ready for the new run.

• The instrument proceeds to run setup when staggered start is available.

When setting up the new run, the software automatically pauses and resumes the run on the adjacent flow cell as needed. The system is placed in a safe state when paused.

See the Staggered Start of Runs section of NovaSeq 6000 Sequencing System Guide for more information.

For any feedback or questions regarding this article (Illumina Knowledge Article #2324), contact Illumina Technical Support [e-mail].