This post (and others like it) are pure speculation from me. I have no insider knowledge and am trying to make some educated guesses as to where technologies like this might go
This is number three in a series of MiSeq posts focusing on what we might get out of the system as it evolves. I originally suggested in my very first post that a 25GB output might be possible, and revised this with some comments on very long 1000bp runs. Our last flowcell generated 2.24GB from a PE151 run and we continue to get very high-quality data and good yields (when the instrument works). Recently Illumina announced improvements to the MiSeq and suggest 7GB will now be possible using a combination of more imaging and longer reads (PE250bp).
I have created a little spreadsheet that allows you to play with read numbers and how much flowcell gets imaged. I am sticking with my assumption that a MiSeq flowcell is around one third of a HiSeq lane, but of course Illumina might increase the width of the MiSeq lane and further increase data output that way.
The spreadsheet gets 7GB from a 250bp paired-end run so confirms what Illumina announced (I'll take this as a sign that the spreadsheet works!)
Using the default 300bp run we should get 2, 4 and up to 12 GB from a run as more surface area gets imaged.
If we move to 250bp paired-end runs (500bp) and increase clusters to 10M over the current 7M average then these numbers jump quite considerably, but not beyond reason. It looks like 5-30GB could be possible with additional tweaks. The 30GB output would be some 80M reads. Quite a lot from a little box!
I'd like to see 1000bp reads, even in the form of "mini-contigs" from PE550bp.
What would you do with 60M 1000bp reads? There were almost 6M whole-genome shotgun reads used in the Human Genome project, of similar length.