Consider the title of this post. Illumina just spent two times more on PacBio in 2018 than they did on Solexa in 2006. $1.2 billion on a technology that many would say is under huge pressure from @ONT, and is a company burning cash fast…very fast. These are two very different companies and the buyout may include a few wrinkles yet to come. However, there has been real development in the hybrid-assembly space where combinations of Illumina short-reads with PacBio long reads leads to a significantly better genome. So Illumina seem likely to push an Illumina/PacBio hybrid as the new normal. I think a stand-alone single-box system is something I pretty unimaginable!

Unlike Solexa – a UK company starved of investment and struggling to commercialise, PacBio has had a reasonable amount of cash to invest in the platform over many years and has delivered real developments in the technology, albeit slower than many users would have liked. Is it possible for Illumina to make such a splash as they did with Solexa in making a “PacBio for the masses”? I guess we’ll have to wait until at leat mid-2019 to see! (Read Theral Timpsons coverage on Mendelspod. Nothing from Keith or Dale yet.)

Is $1.2B a big number for Illumina: Illumina made $830 million in Q2 2018. That is 30% more than they paid for Solexa in 2006, each quarter. Stop and think about that. This has been done on fantastic margins so Illumina is rich and capable of spending big. But it has been a decade since Illumina transformed genomics by purchasing Solexa and it is not clear that this deal is going to lead to benchtop Sequels or all of us using PacBio rather than SBS! This deal is not the same as Solexa.

The horses mouth: FDS and MH spoke for 12 minutes on Illumina’s conference call to investors and nearly all the discussion was on combining short and long reads. FDS started by saying that SBS remains the platform of choice for majority of users going forwards (true). But that long-reads are important and complementary (also true), hence the purchase of PacBio. FDS mentions PacBio’s 15-30kb reads and they’ve done some great work in the last couple of years in pushing the technology forwards (as per Jonas Korlach’s announcements at AGBT2017 and AGBT2018) increasing output by another order of magnitude. But can Illumina take this to another one or two orders? On the call FDS said they were doing it [the deal] to broaden the use of NGS and that there were several strategic reasons 1) expand markets in plant and animal, transplant and functional genomics – together a $2.5B market in 2022. 2) Better SVs improves studies of rare disease oncology and clinical microbial sequencing in phased genomes. 3rd the nest technologies. Broaden access to PacBio via Illumina’s sales and support teams – but still need to sell boxes to labs. Both companies will continue to operate as completely independent until the sale has gone through.

FDS said two other things on the call that caught my ear. Firstly that “lots of large centre customers have a PacBio” – yeah but most small customers don’t and would not! Second that “the deal buys a technical team with single molecule and nanopore experience” how quickly will Illumina start suing ONT? PacBio just stopped one law suit.

No one mentioned ONT are now at 2Mb+ nor BGIs $100 genome sequencer.

How did Twitter react?

Well Clive chipped in quite quickly…something I can’t see FDS or JF ever doing!

Nick was speechless but surprised.

And I love to quote Gavin Sherlock here, remember his “cluster fuck” comments!?!

In summary: is this good for the NGS community? I am not quite sure. It means users will be more likely to run hybrid assembly projects and that is going to be good for science. PacBio might get a significant boost in R&D and sales and support so that’ll be good too. But it means Illumina have an even tighter grip on the field and many users are already unhappy with limited choice…and a company becoming a little bit more like ABI every day. Remember “The more you tighten your grip, Tarkin, the more star systems will slip through your fingers”.

PS: how many MinIOns can you fit in 1x NovaSeq + 1x Sequel? Over 20,000!

PPS: Why did @ChrissyFarr use a picture of Jay and not Francis?