Cluster density guidelines for the MiSeq
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
*Using PhiX library (~500 bp) as reference
Best practices for sequencing low diversity libraries:
• When running low diversity or unbalanced libraries it is recommended to
reduce the library loading concentration to target a cluster density
3040% beneath the optimal range for the chemistry version and
platform used. The optimal amount of reduction required must be
empirically determined.
• To compensate for low base diversity in libraries, Illumina recommends
spiking in a minimum of 5% PhiX Control v3 Library for sequencing.
PhiX has a diverse base composition (45% GC and 55% AT that
provides the balanced fluorescent signals that low diversity sample
libraries lack during each sequencing cycle.