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: