What is cluster density?

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Cluster density refers to the number of DNA clusters per unit area on an Illumina Next Generation sequencing instrument flowcell. The unit of measure is “K/mm2“, or thousands of DNA clusters per square milimeter.

This is a critically important metric because it determines the amount of sequencing data that can be generated from a flowcell. A higher cluster density results in more sequencing data, but also requires more careful management of the flowcell to prevent overcrowding and other issues. Illumina flowcells are designed to have a certain optimal cluster density, and the process of preparing samples for sequencing involves adjusting the amount of DNA used to achieve this density.

Fig. 1.  Illumina MiniSeq flowcell.

For example, on the Illumina MiniSeq sequencer, the optimal cluster density is 170-220 K/mm2. This cluster density will yield the highest quality results and greatest throughput on the sequencer.  If the cluster density is < 170 K/mm2 or > 220 K/mm2 the quality of the sequencing results will decline, although there is a fairly large range of lower and higher densities that will still yield very usable results.  However, note that extremely low or high cluster densities will cause a run failure, so it’s quite important to strive for the optimal cluster range when loading the flowcell.