What factors impact the total number reads produced by different sequencing instruments (e.g. HiSeq vs MiSeq)?

Question

[toddknutson]

I understand that different Illumina sequencers can output different numbers of reads (i.e. HiSeq instruments can produce 40-400 million reads/lane, whereas MiSeq can produce 5-25 million reads/lane). My question is why? What factors in the Illumina next-generation sequencing technology impact read count outputs from these sequencers? For example, can certain instrument settings increase or decrease the number of reads produced (assuming that equal amounts of DNA were supplied to the sequencer)?

Answer 1

[harold.smith.tarheel]

The two factors that limit the amount of data are 1) the maximum cluster density (i.e., number of clones) that can be imaged and resolved by the camera, and 2) the surface area of the flow cell lane that's imaged (MiSeq flow cells are much smaller than HiSeq).