How to troubleshoot clustering failures on the NovaSeq X Series

Background

Issues with clogs in the fluidic lines or consumable quality can impact clustering and sequencing fidelity on the NovaSeq X Series. This can lead to severely reduced clusters passing filter (%PF), low quality scores, and increased PhiX error rates across some or all lanes of the flow cell.

If a clustering issue is suspected, collect the following files and contact Illumina Technical Support for next steps.

1. Collect the run metrics files from the Sequencing Run Output folder:

   1. RunParameters.xml

   2. RunInfo.xml

   3. InterOp folder

   4. InstrumentAnalyticsLogs folder

   5. Logs.zip (Located in the Logs directory within the Run folder)

2. Confirm whether the LYO vials in the Reagent Cartridge used for run are full or empty after post run wash.

3. Confirm if the residual volume in the Library Strip Tubes are even across all 8 individual lanes.

For any feedback or questions regarding this article (Illumina Knowledge Article #8328), contact Illumina Technical Support [e-mail].