The upcoming Proton PII and the NextSeq 500 11

Record PI runs with a 20.5GB at the top, from the Ion Community site

Record PI runs with a 20.5GB at the top, from the Ion Community site

There has been a lot of publicity around the NextSeq 500 from Illumina, and it appears to have been designed to compete directly against Ion Torrent’s upcoming PII chip. Thanks to a visit to upstate New York last week, I met Dr. Sridar Chittur who told me how important it was to put current information out on this blog, and if I can put out the disclaimers up-front it would be very helpful for those thinking about what benchtop system to purchase over the next several months.

First of all, the upcoming Ion Torrent Proton PII is coming out later than expected. We were told (and told customers) when the PI came out in early 2013 that the PII would be six months after the launch of PI.

Where is the PI now? Today customers routinely get 70-80M reads per run, at a readlength on the order of 150+ base-pairs long, or at least 10GB of data per run.

If you access the ‘Run Recognition’ section of the Ion Torrent Community, the highest throughput PI runs are currently (as of March 2014) 20.5GB, the longest perfect alignment is 334 bases, and the maximum number of reads tops 108.8M. These ‘leaderboard’ numbers will give you an idea of how the best runs are performing, while the throughput of a nominal user will steadily increase to where the best runs perform over time.

On top of this is the promise of longer reads and higher accuracy. A new enzyme called HiQ™ is in early-access testing; information about all of our early-access testing programs that also include Rapid Isothermal Amplification along with a 16S metagenomics solution is found here. At AGBT we reported that this HiQ enzyme reduces insertion errors about 60-70%, and deletion errors on the order of 30%. Ion Torrent will initially release HiQ for the PGM and its 3-series chips, with PI and PII after that.

The PII chip is currently in development, and PII chips have been manufactured and produce data. Alan Williams (head of Ion Torrent R&D) presented this at AGBT, where he stated that key milestones have been met (in particular getting a 5 gigabit data throughput off the chip into the Proton electronic architecture, no mean feat as that represents the equivalent of 50,000 simultaneous HD television streams). However he was only able to show a representative 1/16th of the existing iteration of PII chip, and some minor engineering optimizations are needed before a PII chip can be commercialized.

Ion Torrent expects the PII chip to enter early-access this summer (2014), and commercial launch would depend upon those results.

But even data from 1/16th of a chip (presumably the ‘best’ 1/16th slice) is telling – a 91bp and 119 modal readlengths from two human DNA fragment library runs, and a 77bp modal readlength from a whole-trancriptome (RNA-Seq) run. Extrapolating the number of reads to 16/16ths (and entire chip), the number of reads ranged from 296M to 342M reads. (Compare this to an expected read number of about 240-320M for the PII, and for the curious the current PDF of the Proton System spec sheet is here.)

The difference between PI and PII is that the PII has four times the number of wells (increasing from some 165M to 660M), and a corresponding decrease in the size of the Ion Sphere Particles™. Given the number of reads on the PI started in the low end of the 60-80M reads/run specification, let’s presume the PII launches with about a 240M read/run (low end of 240M – 320M range), and about 100bp readlengths.

What does this mean for the end-user, and how does it compare? Let’s look at whole-transcriptome sequencing first, where read number is paramount rather than total throughput in basepairs.

The Proton will output 240M reads in 4h, at a cost of $1,000/run. (Clarification – this is only sequencing time, not template preparation plus sequencing time, so the template plus sequencing time is about 8 hours.) On a cost-per-million reads basis, this is 1/4th the cost of the existing PI chip (the PI chip also costs $1,000/run for 60-80M reads). The new NextSeq 500 in its most efficient ‘high throughput mode’ is $4,000/run for 400M clusters, presumably slightly less expensive for single-read instead of paired-end, and also slightly less expensive for shorter reads for fewer SBS cycles, but major costs are in the clustering and flowcell pieces. Even if that price is reduced to $3,500/run for 400M single-end, 1×75 bp reads, that’s still a good $875 per 100M reads on the NextSeq, whereas the PII prices out at $416 per 100M reads (that is, $1,000 / 2.4 x 100M). So there’s a 2x markup on a per-read basis. And the time for template preparation (that Illumina calls clustering) plus sequencing is 15 to 18 hours.

So the appellation “cheaper to buy, cheaper to run” holds for the Proton. (The comparable system list prices are $239K for the Ion Torrent Proton versus $250K for the NextSeq 500; there is a low-throughput mode on the NextSeq 500 that lowers the cost to run the instrument but at a relatively high per-read or per-GB cost.) You can also add “faster to run” too – about half the time.

What about on a whole-exome basis? Here the PII will be at a disadvantage as the Ion AmpliSeq Exome needs the 230-250bp readlengths as mentioned earlier, and it will take some time to optimize and develop the PII sequencing to get basically double the readlength from launch. There isn’t much doubt that this will improve over time, just like the PI and the 3-series chips on the PGM (314, 316 and 318) before that.

What about sheer per-GB cost at the PII launch? At 240M reads and 100bp readlengths, that represents a throughput of 24GB for $1,000/run. The NextSeq 500 in ‘high throughput mode’ (that is in the most efficient sequencing mode 2x150bp paired-end reads), the yield is 100GB for $4,000. So at launch the per-GB cost is essentially the same, and when AmpliSeq Exome attains a 250bp readlength the relative price differential can easily be 2x. (You can be assured that the NextSeq 500 will increase its readlength and density over time, however at what rate remains to be seen.)

Chart comparing the Proton PII and the NextSeq 500

Chart comparing the Ion Proton PII and the Illumina NextSeq 500

So I’ve put together this simple chart, which summarizes what I’ve written out above, based upon some straightforward reasoning. I can go on and on using fear, uncertainty and doubt about the NextSeq 500’s base-calling of G residues on the basis of an absence of signal, but instead would take this moment to point out that it will take many months of effort and modified (or altogether new) tools to adjust to a new instrument and new chemistry, when users choose not to use the vendor-supplied software pipeline tools. This is similar to when the Ion Torrent PGM first arrived and complaints arose regarding poor-quality data when aligners other than TMAP were used, as they were tuned for a different platform. I remember early users using GATK and being very dissatisfied with their results.

Lastly, a note of observation.

The world of consumer behavior has changed enormously with the wide availability of information. It wasn’t that long ago when if you wanted to find out about a new product there were limited channels of communication; now it seems like everyone has an opinion and are willing to take the time and energy to share them. There seems to be something of an explosion of anonymous blogs, where who is behind it is impossible to determine, by design.

And now in addition to anonymous blogs, there are experts who make commentaries on a sequencing technology conference (namely AGBT) they didn’t even bother to attend; there is an individual writing Twitter messages as if it was her own yet with questionable science credentials; and there are yet others who rip content off from others just to monetize traffic to their website.

It’s a bit of a sad state of affairs with such low barriers to entry. (All it takes is some time and effort behind a keyboard.) There needs to be more genuine, authoritative voices that are quality, original sources of information.

About Dale Yuzuki

A sales and marketing professional in the life sciences research-tools area, Dale currently is employed by SeqOnce Biosciences as their Director of Business Development. For additional biographical information, please see my LinkedIn profile here: and also find me on Twitter @DaleYuzuki.

Leave a comment

Your email address will not be published. Required fields are marked *

11 thoughts on “The upcoming Proton PII and the NextSeq 500

  • PastelBio

    Hi Dale, given that the thrust of this blog is to ‘be helpful for those thinking about the purchase of a benchtop sequencer over the next few months’ and with the PII being projected as a potential competitor to the NextSeq500, wouldn’t it have been useful to give the new timelines for release of the PII rather than just saying that it has been delayed (which we all know already). This may be the most informative piece of information given that if the delay is another 6 months, 12 months or 2 years it could make a sig. difference.

    I would like to know the release date of the PII for different reasons (proteomics based) but I’m sure many of your readers would join me in asking for this important omission to your article.

    • Dale Yuzuki Post author

      Thanks for the input. The PII chip is expected to become available in early access this summer, and for an official launch it would depend upon the performance of the chip at that point.

      Sorry about that omission – a function of late-night writing, and the post has been updated.

  • BigTA78

    Your NextSeq prices are incorrect. The prices I have been quoted for NextSeq run reagents are around $1700 list price for a 75 cycle kit. So cost-per-read and cost-per-Gb will be similar to the PII.

      • Anonymous

        I think you are incorrect here. I have had quoted to me high-output NextSeq run costs, with the 1×75 being $1,300; 1×150 being $2,500 and and the 2×150 being $4,000.

          • Anonymous

            I think the PII has lots of room to grow. Simply (obviously, not so simple) increasing the read length at the same chip cost will push down the cost per nucleotide. Also, once you move out of the large centers, many facilities want the ability to run lots of smaller projects in rapid succession. The NextSeq, with the 400M read unit, does a poor job of this, unless you shift to the higher cost/nuc low output mode.

  • Anonymous

    Here’s the problem with the Proton: the specs are impressive and the price is right, but the chips have been delayed for too long. PIs are really interested in two things: what is the lifetime of this instrument, and is the company committed to supporting it? If you are to look at the MiSeq, that thing has been incredible in terms of new kits and software upgrades (if anyone can even recall its performance when it just started out). On the HiSeq you now have rapid run modes and longer reads later this year. The comparison should be with price and throughput — if a lab/facility can afford these machines and can afford to run them then these differences are marginal — it’s that there is a lack of a clear roadmap and a lot of uncertainty with the Ion platform that makes a lot of researchers hesitate.

    • Anonymous

      Respond to mr/ms anomymous…

      Lets face it.. Illumina is all about comprimizing due to limitations in old technology.. And to be honest.. Stripping down a MiSeq incl downgrading the detection to only 2 color, and having the new unit produced outside illumina factories some where fare east, to save money, just to give space for PII chip capacity, seems in my book a bit desperat, and looks more like a way to try to delay the masive Proton intry to the marked, rather than provide high quality products for their customers..

      The problem, is for many other people, that Illumina is still a major plajor and has good quallity instruments, but does represent the privious generation of NGS technology, and has just put a whole bunsh of instruments on pension incl HiSeq 1000, 2000, 1500, and HiScan. I would prefere a chip version for a few hundred dollors to retire, and be replaced by a new and better one for the same price, rather than my instrument i paid hundreds of thousands for.

      I kind of like the fact that with Ion Torrent, the chip is the machine. According to Life, Ion PGM also has 4 x more publications than MiSeq in 2013, and Ion Torrent represent 52% of the global NGS benchtop marked as Jan 2014, so the game seems to be changing whether we like it or not..

      The Nextseq 500 is, in many peoples mind, if you look at it business wize, really just a highly stripped down version of a MiSeq, in order to squize in Ion Proton PII chip capacity, until the PII chip arrives and will show the same significant development, as seen with all the other 4 chips from Ion Torrent. They did it 4 times before with impressive results, and the semiconductor chip industry, does not seem to run out of power the next comming months, so even with delay, I’m don’t see any reason to worry. If you doubt the lifetime and support on semiconductor chip technology, you might warn your family to drop their smartphones, ipads, digital camaras and Samsung HD TV’s.. 😉

      With Ion Torrent the chip, is the machine, and new chips and chip versions will most likely continiue to arrive, delayed or not, but for the same price as the privious chip versions.. So personally, to make my technology point clear, I would prefere to wait for a new chip for a Proton costing only a few hundred dolors, in order to for example to get access to the $1000 genome, rather than apply for a total project cost at $72 Million, and order 10 HiSeq X instruments, and bind my lab for 72K samples/ year in 4 years, in order to get access to the same $1000 human genome a bit earlier, but with the priovious generation of technology..

      There is space for both the old light-detection based NGS technology and new NGS technlogies in the marked, but for now the new Ion Torrent semiconductor chip NGS technology, is already very well established and has proven its worth, so exciting to se how the marked will develop.. 🙂 Sure illumina has more improvements and technology compensations to develop in order to compete, but looking in to the future from my glases, I wont put my hat on light-detection based NGS technologies.

  • Shawn C. Baker

    Thank you for linking to my interview with Theral Timpson of Mendelspod. ( You are absolutely correct that I didn’t attend AGBT. I think it’s a great meeting, but we just couldn’t manage to make it this year. But I’m not sure how that’s relevant. AllSeq serves as an advisor to Mendelspod on NGS and genomics. As such, we advise them throughout the year on the various genomics and NGS-related interviews they conduct. In addition, once a year Theral interviews us to get our opinion on the NGS market and where it’s going. Many people value that opinion as we have an unusual position in this market in that we’re absolutely neutral – we don’t own any sequencers and we don’t work for a company that makes any sequencers. This allows us to follow this industry and report on it without an agenda. We gather information from many sources – the researchers and providers on our marketplace (, NGS vendors (both on the R&D and commercial side), scientific conferences (some of which we attend in person and some of which we observe via twitter and blogs), market analysts, etc.
    The interview that you’re referencing was an overview of the market, not a review of AGBT per se. It was, however, timed to occur right after AGBT since this is such an important meeting that often has a lot of updates from the platform vendors. This year was no exception, so I was happy with the timing and grateful for the tweeters and bloggers (such as yourself) who reported on the meeting and shared their insights. Apart from your displeasure at my commenting on information revealed at a meeting I didn’t attend as part of an overall market review, was there something specific that I said that you didn’t agree with our thought I got factually wrong? If so, I’d be happy to address it.


    Shawn C. Baker
    CSO, AllSeq, Inc.