MiSeq vs HiSeq flowcell

So here it is, I was given one of these at AGBT and there is a picture in the MiSeq brochure. I thought I’d share an image with anyone wondering what they look like.

You can see it is very different from a HiSeq flowcell in that it is encased in a plastic housing. You can also see two inlet ports just above the ‘um’ in Illumina. These allow the much shorted and therefore faster fluidics to operate. The flowcell lane is bent back on itself, which is difficult to see in this picture.

I believe that only a portion of the MiSeq lane is imaged right now. But I am not exactly sure how much and this is key to working out how much data MiSeq might ultimately yield. A side-by-side comparison to a HiSeq flowcell shows that there is about 1/3rd the surface area of a HiSeq flowcell lane. Cluster density is being reported as the same on both platforms so if the clusters per mm2 is the same then a full MiSeq lane should generate about 1/3 the yield of a HiSeq lane.

However you could not access the increase in imaging area without spending more time on imaging. If Illumina and users are willing to increase the imaged area then yields will go up. MiSeq only images one surface right now, imaging both surfaces would generate a two fold increase but would double imaging time. If MiSeq is currently imaging one ‘surface’ from a possible two and one ‘tile’ from a possible three then it may be possible to increase out put by 6 fold. Of course I am not sure if this is  possible and it relies on my assumptions about how MiSeq imaging works.


MiSeq is sold with very fast run times as a unique selling point and a single end 36bp run takes about four hours. If both surfaces can be imaged and three tiles rather than one are possible then the SE36 run time would go up to 6-8 hours but yield would jump from 0.3GB to 6Gb. For paired end 150bp runs this time would go from 1 to 2 days and yield would rocket from 1.5Gb to 9Gb. Run costs would not change.

I’d quite like my MiSeq to be shipped with a dial in the software that allows me to maximise data in the time I have available. If a run is going on overnight or the weekend for instance then why not let it run for longer and generate more data. This would be essentially for free.

More food for thought.

And ‘Yes’ that is James Watson’s signature on a HiSeq flowcell.