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): 

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: