08/23/2022
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):
Platform | Mode/Reagents | Optimal Raw Cluster Density |
---|---|---|
HiSeq | High Output, v3 | 750-850 K/mm2 |
High Output, v4 | 950-1050 K/mm2 | |
Rapid Run, v2 | 850-1000 K/mm2 | |
MiSeq | v2 | 1000-1200 K/mm2 |
v3 | 1200-1400 K/mm2 | |
MiniSeq | Mid and High Output | 170-220 K/mm2 |
NextSeq 500/550 | Mid and High Output | 170-220 K/mm2 |
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: