Sequencing Instrument Outlook 2026

Beginning of a new year - time to stick my neck out and opine on what the year might hold for sequencing instrument companies and what sort of topics I can already anticipate covering this year.  The J.P. Morgan conference is this week and we're eight weeks from AGBT in Orlando.  Which seems even shorter to me since I'll be focused, with the rest of the Ginkgo team, on touting our autonomous laboratory concept at the SLAS conference in early February - which is in Boston just like ASHG and AMP were in the fall.  Boston really jackpotted on major conferences of relevance!

Roche

Roche's Axelios 1 instrument using Sequencing By Expansion (SBX) technology is certainly going to be a dominant driver of sequencing news this year.  I'm hardly going out on a limb to predict that Roche, while  scoring only a Silver sponsorship, will fully announce their launch plans at AGBT. 

The key bit of uncertainty around Axelios 1 is the consumable pricing strategy.  Roche could go with a conventional lineup of kits, but the nature of the platform could support other approaches.  In a kit form, we'd likely see kits for expansion chemistry, nanopore array, sequencing operations and nanopore array regeneration.  But the variable run time of the system could also lend itself to some sort of sequencing metering approach - literally paying by the gigabase of data.

One should also not be surprised by further improvement in the sequence quality metrics - likely due to further refinement of bioinformatics for base and variant calling and perhaps run times.

The Roche team is single-minded on getting their system successfully launched - I've been in the the room when some fool tried to suggest a direction for iterating the instrument design to integrate into an autonomous laboratory scheme and the project lead has been adamant about maintaining a strict focus on getting the system out the door.  So we probably won't see much from Roche this year on a second generation system - though Roche engineers are almost certainly working internally to create a fully automated Axelios-based high throughput diagnostic system to complement their cobas qPCR system.  That both the instruments in Axelios - the expansion chemistry unit and actual sequencing unit - are basically liquid handling robots under the hood should make this relatively straightforward - and is the same route that fool was thinking of for autonomous laboratories.  But that probably all waits until 2027

Illumina

Illumina certainly will be watching Roche's pricing strategy with great interest, but will on their own be a driver of much news.  Illumina is trying to convince the 'omics community that all their critical needs can be handled with an Illumina instrument and then one of Illumina's kits - Constellation for long range genome information, Illumina bulk RNA, Single Cell, and spatial transcriptomics for RNA studies and Illumina Protein Prep for the proteome, all tied together with Illumina Connected Analytics bioinformatics workflows.

How well those pieces are really connected remains to be seen - and how connected can they be?  That deserves a more in depth analysis, but to give one example Illumina Protein Prep covers a wide range of proteins seen in serum, but not all the intricacies of proteoforms that might better inform intracellular analyses.

It's also the case that each of these products is entering markets which already have strong incumbents.  Constellation must steal market share from PacBio and ONT.  10X Genomics already has a strong position in single cell, with other players such as QIAGEN (via their acquisition of Parse) and BD.  10X similarly has a strong position in spatial, with Bruker/Nanostring another big player.  So all of these areas will be interesting to watch as Illumina tries to muscle in on the strength of their product and their salesforce selling the idea of one-stop-shopping.  Protein prep is the exception here; Illumina is holding half of what is essentially a duopoly in the high throughput protein profiling by DNA sequencing market. 

On the hardware front, Illumina is settling down on the trio of MiSeq iSeq 100 for the low end, NextSeq in the middle and NovaSeq X at the high end.  I'm not expecting that to change, with Illumina mostly focused on weaning users away from older instruments that are fading away, such as the MiniSeq and classic MiSeq.  Some new capabilities are being rolled out in terms of new sequencing modes - such as 2x500.  My wet lab colleagues had been advising to avoid on patterned flowcells inserts bigger than 500 bases, so it will be interesting to see how this meshes - I'd find 2x500 most interesting if there's only just enough (100?) bases of overlap to merge the reads.  Perhaps the 2x500 flowcells have bigger nanowells to fit longer library molecules?

PacBio

The major question around PacBio is financial: can they pull out of a pattern of 5 quarters of not even flat revenue.  By my completely naive calculation (I just divide cash-in-bank by reported loss), the company treasury will run dry in eight quarters.

On the hardware front, Revio and Vega seem to be making a good pair and Vega units are selling well - but neither line is generating the requisite revenue pull-through.  PacBio is reputedly still working on an ultra high throughput instrument, but given the current state of customer demand an even more powerful instrument might be a revenue disappointment - unless dropping the cost per genome further suddenly unlocks significantly more demand.

PacBio is rolling out limited flowcell reuse, which should drop the price of datasets, so that will be an early test of the thesis that further reductions in data generation cost will drive greater adoption.

But Illumina's Constellation represents a possible headwind.  How many labs wanting to perform whole genome sequencing will decide to go with Constellation to run on their existing NovaSeq X rather than investing in a Vega?  That's a question which should be stealing sleep from PacBio executives.

PacBio also might experience headwinds from Roche's launch if long read RNA-Seq, single-cell or bulk, ends up shifting to the mid seq lengths on Axelios - far more reads even if full mRNAs aren't always read.

PacBio also keeps expanding support for additional assays.  For example, marketing PureTarget as a means to supplement short read genomes or exomes with hard-to-call regions. Another application vulnerable to encroachment from Constellation - unless of course PacBio can convince labs that Constellation isn't trustworthy for these regions.  PacBio has partnered with EpiCypher, who is offering a Fiber-Seq assay kit for marking histone occupancy onto long reads (as I covered back in May 2024)

Oxford Nanopore

In my last piece on ONT, I put forth that the company was executing a well thought out succession plan at the second tier, with experienced insiders Rosemary Dokos and Lakmal Jayasinghe covering product and technology respectively and that this would make CEO Gordon Sanghera's retirement less risky.  But before a new CEO was announced, Dokos announced she was leaving the company, blowing up my thesis 

We also now have a CEO named, Francis Van Parys.  who will take over at the beginning of March.  Based on his LinkedIn profile, Van Parys has some experience in diagnostics but nearly none in genomics.  He started with almost eight years in commercial roles on the non-life science side of GE.  He spent 11 years in GE Healthcare, and was "Global Product Management Leader, Consumables" for a year and a half and 3 years as "GM Product Management, Research & Applied Markets" - that consumables business includes the ampliPhi Multiple Displacement Amplification reagent used primarily in genomics, so that can be scored as some exposure to the space. He stuck around for a bit over 3 years after GE Life Sciences was sold to Danaher and rebranded as Cytiva.  Since Jul 2023 he's been president and CEO of Radiometer, which he describes as holding "a market leading position in Point of Care Diagnostics in acute care settings".  

Every new CEO should be given some breathing space to learn the organization and product line, so perhaps we won't see radical changes enacted by Van Parys in 2026.  But the Board of Directors choosing a complete outsider to the space is interesting, particularly in a company such as ONT with such an inward-facing culture.  Will any major changes be visible prior to London Calling or made clear there?  Is Van Parys a punk rock fan or will the London Calling soundtrack change radically?  These are questions that will certainly make for an interesting meeting yet again.

 

Cleaning up a loose end but appropriate here, in my last piece on ONT a commenter asked me about a comment I had made on PromethION.  I had to search for it - saying it might be a "bridge too far" did ring true since I've read a bit on Operation Market Garden (and hiked around Arnhem, including the replacement for the bridge whose full control eluded the Allies) - and it turns out I did have a piece titled "Is PromethION a Strategic Error?" back in November 2016 with that phrase!  I'm impressed that some readers have such memories for what I wrote!

And it has me wishing I kept better score and gave more frequent updates on my calls.  Clearly PromethION is a success - though it also certainly took a lot of time to get to a fully working system and some of my concerns of the time - such as issues around which flowcell classes were available on PromethION - IIRC these did play out.  Perhaps the bigger "what if" concerns the somewhat inverted evolution of the product line - the more complex P24 and P48 were attempted first and only much later the far simpler P2 units - and P2 is what is perceived as driving much of the success.

ONT probably has the least to lose to Roche, since its never really developed strong presence in the short or midi read spaces, despite sometimes claiming to have capabilities there.  Constellation may crimp further penetrance into clinical whole genome sequencing - or at least further muddle this market.

ONT reports revenue by halves, and also has a bit of flat revenue problem - H1 2025 was about on par with H1 2024 with H2 2024 being a dip. As a commenter pointed out, I got this wrong - 2023 into H1 2024 was very flat but there's been growth since - but we haven't seen final 2025 numbers.

Ultima

Ultima is another company with questions over finance - but since it is private there's complete opacity as to how good or bad Ultima's balance sheet is.  Developing a new sequencing platform and then launching it never comes cheap.   So Ultima will likely need to raise money either this year or next.  That could be another round of fundraising, a strategic investment, IPO, or being acquired.  Or the grim alternative of going away.

I list the last for completeness; I believe Ultima has built enough of a customer base to be an asset that would not just be allowed to disappear ala Genapsys.  Ultima has gained a number of customers in the high throughput diagnostics and human genomics space - getting MyHeritage to switch from arrays to Ultima last year was a serious coup.  The fundraising and IPO markets still seem to be weak for molecular tools, so more likely by my reckoning that it will be a strategic partnership or being acquired.  Big molecular tools conglomerates such as ThermoFisher, Danaher and Agilent have large market caps and deep pockets - might we see some action here?

Ultima risks being the most affected by Roche launching.  UG100 is a big pair of boxes that generates huge amounts of data which costs about 2X what Roche is selling Axelios for.  Should Roche price the consumables very aggressively, Ultima would be in trouble.  That seems unlikely - the profit-maximizing price for Axelios data is probably much higher than the $70 for 100Gb that Ultima has (at least last I remember; perhaps it has dropped further)

Element

I thought about lumping Element with Ultima because much of the story is the same - a private company with opaque finances.  So the same language on a likely need for financing and possible financing routes applies.  Similarly, I believe Element has built enough of a user base that they would be acquired rather than being allowed to disappear - Singular was acquired despite a much smaller install base.

Element sees the big value in their multiomic profiling capabilities, which also takes them largely outside Roche's shadow.  I'll confess I don't know what sort of penetration Element is making within pharma, in part because to estimate it I would need to go to very different conferences than ASHG and AGBT.  

Complete Genomics

Complete Genomics always represents a challenge for covering - very interesting technology but always under the shadow of US-China relations.  Complete always claims independence from BGI and the Chinese government and always receives skepticism from both users and the US government.  Complete freed of this issue would certainly compete much better with Illumina et al.  But that is the reality - no matter how good the technology, many won't invest for fear of future disruptions

New Entrants, China & Other Loose Ends

Rounding things out, there is always a chance (hope?) of new entrants.  There aren't any obvious ones on the horizon, but I have been humbled by Ultima and Roche in my belief that I'll know early about anything brewing in this space.

China is increasingly a hotspot for new sequencing companies.  Most of these seem to not be innovators, repackaging existing technologies (perhaps not respecting extant patents in doing so).  Nava Whiteford over at ASeq does a good job of keeping tabs on these.

DNAe (formerly DNA Electronics) is moving to launch a product, but straight to the point-of-care diagnostics market with a sample-to-answer system.

On a similar note, I've left Thermo Fisher's Ion Torrent technology off my radar for a long time, but I'm acquiring a new appreciation of their Genexus sample-to-answer platform using Ion Torrent technology.  One interesting notion floated by someone on the ASeq Discord would be Thermo acquiring Element to swap into Genexus.

What did I miss?  Where am I wrong?  What other old predictions do you want to call me on? I actually prefer brickbats to kudos - they're much more interesting!