Best practices for starting staggered runs on the NovaSeq 6000
Users can set up and start a run on the idle side of the instrument while a run is in progress on the other side, which is referred to as a staggered start. Staggered runs are set up at specific times during a run, as indicated by the following countdown timer states.
Run Start: Available: Staggered start is currently available. The date and time show when the staggered start will become unavailable. Select Sequence to start a new staggered run after the current cycle is complete.
Run Start: Unavailable: Staggered start is currently unavailable. The date and time show when the staggered start will be available on the other side of the instrument.
Waiting...: If a new run is attempted when the 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 will proceed to run setup when the 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.
The staggered run start will be unavailable during the following times:
Cluster generation.
Imaging.
Paired-end turnaround.
Washing.
The user must wait for these to complete for Run Start: Available.
Procedure:
From the Home screen, select Sequence, and then select A or B. The selected side must be the currently idle side.
Wait for the run on the adjacent flow cell to pause. To cancel the new run and prevent pausing, select Cancel. If the adjacent run is performing cluster generation, paired-end resynthesis, imaging, or washing, the software completes the current step before pausing.
When the adjacent run is paused and the flow cell door opens, set up the new run. When the new run is started, the paused run is automatically resumed and then the new run begins.
Best practices:
If loading two Xp runs, start one run and then stagger the second (only prepare the libraries when the other side is available to stagger).
Important Note: Illumina recommends against setting up two Xp runs at the same time. The Xp workflow is less tolerant of delays in starting the run (including due to pre-run check failures, such as an issue with disk space, network, flow cell seating/debris, etc.). To restart the side that failed, the user must wait for 2 hours for the running side to finish cluster generation before stagger starting the side that failed. This delays the Xp run that must start within 30 minutes after loading libraries onto the flow cell.
If running Standard and Xp together and need to stagger, Illumina recommends starting with the Xp run first.
The staging time for loading libraries using the Xp workflow onto the flow cell is sensitive to starting within 30 minutes.
Do not disturb consumables on paused side of the instrument, as this can result in loss of the run.
For more information, refer to NovaSeq 6000 Sequencing System Guide.
Note: For NovaSeq control software versions before v1.4, the instrument must be idle to start an Xp run due to sensitive staging time. Do not start an Xp run as a staggering run.
If an Xp run is in progress and the other side is idle, it is okay to only start a standard run.
If setting up an Xp run and a standard run, press start on the Xp run first.
Avoid setting up two Xp runs at the same time. Current recipes can cause delays on the run that started second, which can lead to run failures, low % occupancy, and %passing filter irregularities.
For any feedback or questions regarding this article (Illumina Knowledge Article #6202), contact Illumina Technical Support techsupport@illumina.com. |
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