Opiniomics

bioinformatics, genomes, biology etc. "I don't mean to sound angry and cynical, but I am, so that's how it comes across"

What does the PacBio Sequel mean for the future of sequencing?

PacBio have responded to intense competition in the sequencing market by releasing the Sequel, a machine that promises 7 times the throughput of their last machine (the RSII) at a price of $350k (the RSII cost more in the region of $750k). So they have a cheaper, higher throughput machine (though I haven’t seen cost-per-Gb figures).  That’s around 7 Gigabases of reads averaging around 15Kb in length.  Without doubt this is a very interesting platform and they will sell as many of them as they can produce.  A sweet spot for assembly is still 50-60X for PacBio, so think 12 SMRT cells to get a human genome: let’s say £12k per genome. Edit 01/10/2015 my maths at 7am was not that good!  50X human genome is 150Gb, so that’s 21 SMRT cells and £21K per human genome.   Much more expensive than Illumina’s $1000 genome, but far, far better.

I just want to say that at times I have been accused of being an Illumina- and a nanopore- fanboy; I am neither and both.  I am just a fan of cool technology, from microarray in the 90s to sequencing now.

In long reads, let’s be clear, we are talking about the promise of Oxford Nanopore vs the proven technology of PacBio.  And the Sequel changes the dynamics.  However, the MinION fast mode is capable of throughput in the region of 7Gb (like the Sequel) and the PromethION is capable of throughput on Illumina-scale.   Therefore, Oxford Nanopore are far from dead – though they need to respond.

So how does the new PacBio Sequel change the market?  A lot of initial reactions I have had are that the Sequel is a real threat to Oxford Nanopore.  It certainly ramps up the competition in the long read space, which is a really good thing.  But actually, high-throughput long read machines like the Sequel and the PromethION don’t spell the end for one another – they actually spell the beginning of the end for Illumina – as a sequencing platform.

As soon as you have high-throughput, cheap long reads, it is in fact Illumina who face a problem.  I love Illumina.  When I first arrived at Roslin, I walked into our lab and (honestly!) stroked our Illumina GAIIx.  Illumina have revolutionised biology.  However, short reads have limitations – they are bad for genome assembly, they are bad at complex genomes, they’re actually quite bad at RNA-Seq, they are pretty bad for structural variation, they are bad at haplotypes and SNP phasing, and they are not that great at metagenomics.  What has made Illumina the platform of choice for those applications is scale – but as soon as long read technologies reach a similar scale, Illumina looks like a poor choice.

The Sequel (and the PromethION) actually challenge Illumina – because in an era of cheap, long read sequencing, Illumina becomes a genotyping platform, not a sequencing platform.

9 Comments

  1. this is good news for the community. pacbio, along with oxford nanopore, represent proven long read technology that will help generate near complete genome and accurate transcriptome assembly. however, the criteria like read length, ability to assemble genomes accurately etc etc are not, imo, going to matter for wider market penetration. cost of the box, the easiness/availability of assay/chemistry kit and access to a winder distributor/support network, are going to play imp role. this is true assuming that the company can raise in an excess of $200million dollars before either going public or getting sold to another company in order to sustain internal research and development. this is an insane amount of money.

    no matter which company wins, none are interested in working towards democratizing global science, i am afraid. they are not making access to the technology early, and making it widely & globally available. companies are restricting access to a certain geography at an early stage (perhaps there are support issues), therefore giving a head start to the researchers in that region. there is far more interesting scientific and societal applications globally that can be resolved using sequencers but early access and access to expert technical help are current obstacles (of course, along w access to money).

  2. Few issues: You say “..the MinION fast mode is capable of throughput in the region of 7Gb (like the Sequel) and the PromethION is capable of throughput on Illumina-scale.” Is that statement of fact that you can back up with data or reiteration of what ONT has said? (if you can call it a fact, I’ll turn red with jealousy and start throwing things 😉

    The application that Illumina still has an edge is counting. Granted that ChIP-exo and Hi-C might be fine with PromethION but stuff like SELEX, where you need to count the ‘correct’ sequences without help of the reference, seems out of reach for single molecule methods (at least for now).

    K

    • As I said in the post, it is the promise of Nanopore vs the proven tech of PacBio. But with ONT, the nanopore is the sequencer, and therefore it is possible to massively parallelise the technology in a way that isn’t possible with Illumina and PacBio.

      I am not sure what SELEX is, but certainly for “counting” RNA (transcriptomics), long reads would beat Illumina every time – providing there is necessary throughput.

      • This ONT really ever have the throughput to accurately quantify transcriptions across many samples/conditions. Will there come a time in the near future when I can assemble sufficient nanopores in parallel to run 30 RNAseq samples on an ONT, with sufficient throughput on each sample to detect 1.5x differences in expression for the same cost/time as illumina? Or assays like HiC, where you need read counts in the 100s of millions.

        I suppose what I’m asking is how long is it going to take for the PromethION to reach illumina-scale throughput (in terms of read counts rather than Mb of sequence) at the same costs?

      • “Massive parallelism” and “nanopores” in the same sentence are yet to be proven compatible. The Promethion is 48 minions in a single box. Scalability is an issue that ONT has yet to explain how they will tackle. Not saying it is impossible, just that it is highly non obvious mostly for hardware reasons. Fast mode is the answer they have provided so far, but when/if it becomes a reality it is a one time bump.

        A question on your PacBio human genome calculation. 3G at 50X coverage at 7G per cell works out to 21 cells not 12.

  3. A few issues here. 50-70x is no longer the sweet spot. cited here:
    http://wgs-assembler.sourceforge.net/wiki/index.php/Version_8.3_Release_Notes
    Algorithms for better assemblies using lower coverage are improving. Also remember this is on 1 smrt cell now not multiple so the biases that existed by using multiple smrt cells is also gone.
    Also the new insert libraries are at 30kb not 15kb.

  4. Why are short reads “bad for genome assembly… complex genomes… RNA-Seq?”
    Thanks,
    Eric

    • Relative to long reads, short reads are bad for these things

      • Don’t you end up with the correct sequence either way? I thought the overlapping areas of the short reads are aligned and you end up with the correct sequence. I don’t understand the advantage that PacIfic Biosciences has by using longer reads.

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