Wednesday, 16 May 2012

HiSeq 2500: how much will the "genome in a day" cost?

The launch of HiSeq 2500 generated a buzz as it came hot on the heels of the Ion Proton. Both instruments will allow users to generate a genome in a day. HiSeq 2500 was launched with a 127Gb in 24 hours spec. Current specs on the Illumina website are at 120Gb in 24 hours, 300M reads and PE150 supported (yielding 180Gb in 39 hours). All this for a $50,000 upgrade fee which makes it seem likely that many users will upgrade at least one instrument.

If you want to know more read the 2500 app note on Ilumina's website, although the Yield figures in the table appear to be incorrect!

There has been much less noise about the likely cost of the data from the rapid run "MiSeq on steroids" format. A recent post on SEQanswers is the first sniff of HiSeq 2500 pricing, although it may not be accurate. It suggests a PE cluster kit will cost $1225 and a 200 cycle SBS kit will be $1690.

I used these figures to get to the possible cost per lane of a HiSeq 2500 run:
  • PE100 multiplexed: £900 or $1500

This compares incredibly well to the normal output. In fact to me it looks like HiSeq 2500 rapid run mode could be the best choice for core labs like mine as it offers incredible flexibility as a two lane flowcell is quicker to fill up than an 8 lane one. And five dual-flowcell rapid runs will take less time and generate the same data as a dual-8-lane-flowcell standard run. The cost per Gb is going to be a little higher but many users will see this as a fair trade-off for faster turn-around-times.

The HiSeq 2500 rapid runs will also use on-instrument clustering. Exactly how this is going to fit inside the instrument with the available fluidics is not completely clear. I'd expect that we will have to run both positions in the same configuration using the current PE reagent rack.

Whether Illumina are able to really turn HiSeq 2500 into "MiSeq on steroids" and up read lengths to the 687bp presented at AGBT is still to be seen. They might have to if Ion Torrent can push their read-lengths out to current 454 lengths.

The competition: The latest specs from Life suggest that the Proton II chip will generate 20x coverage of a genome (and analyse in a day). However it is not clear if the run time will be longer or multiple chips will be run, current times are 2 hours per chip. A 20x genome in 2 hours would be great, but I don't think we can expect quite that from Life just yet. There is also a video of the first 4 Proton's to be installed (at BCM); "install to sequence in 36 hours" although the video only shows samples being centrifuged before loading and no real sample prep.

What's next: One thing I am happy to predict is that advances in sequencing technology are not going to stop any time soon, and when ONT come out from under their invisibility cloak we might finally get a peek at some data that shows what tomorrow holds.


  1. Hello James, I am a science writer @Illumina and was wondering what the mistake is in the yield numbers for the HiSeq app note?

  2. Table 1 is confusing, and as such is what I deem to be incorrect.

    It shows the stats from a run of two flowcells, broken down by lane. The final column then shows the "average/total" but only reports one figure in each row.

    I would suggest a clearer heading would be "run total/lane average" and to have single figures for %PF and Bases Q30 but run and lane figures for clusters, clusters PF and yield.