Cluster density guidelines for Illumina sequencing platforms using non patterned flow cells

Cluster density is an important factor in optimizing data quality and yield. The following table lists the recommended raw cluster densities for balanced libraries (such as PhiX):

The iSeq 100, NextSeq 1000/NextSeq 2000, HiSeq 3000/HiSeq 4000, HiSeq X and NovaSeq 6000 systems utilize patterned flow cells, which result in a fixed cluster density, even if all nanowells are not occupied. In these systems, monitoring the Cluster PF (%) is a better measure of potential cluster occupancy.

Please see the following for further details:

• Plotting % Occupied by % Pass Filter to optimize loading concentration for NovaSeq 6000 and iSeq 100 platform

• Best practices to improve clusters passing filter and yield when using patterned flow cells

• Calculating Percent Passing filter for Patterned and Nonpatterned Flow Cells

For any feedback or questions regarding this article (Illumina Knowledge Article #1511), contact Illumina Technical Support [e-mail].