JPM20 Loose Ends: Agilent, ThermoFisher, 10X Genomics, NanoString - plus PacBio & ONT

Time to close out  J.P. Morgan season with a grab bag of kvetches and kibbitzing on multiple 'omics companies that presented.  Much of this has been stimulated by Twitter discussions, with particular credit going to Varro Analytics and Albert Vilella.   While I've never been to J.P. Morgan physically and am skeptical I'll ever go, reviewing all this is a great prep for AGBT -- which I'm happy to be returning to this year for it's last Marco Island appearance for many years (forever?).

Bold Genapsys Talk at JPM20

Genapsys' CEO Hesaam Esfandyarpour presented today at the JPM Morgan Conference and delivered an expansive vision of where the company is going both this year an the long term.  This includes planned commercial launch of the 144M chip this year, an aggressive expansion into international markets and another round of "pre-IPO" financing.

JPM20: Roche Links with Illumina On Diagnostics

Another bit of Illumina news released at J.P. Morgan today is that Roche Diagnostics is partnering with Illumina.  The 15 year partnership (same duration as with QIAGEN) will place Roche diagnostic assays on Illumina clinical-grade sequencers as well as the two will jointly work for regulatory approval of Illumina's TruSight Oncology assays.  Roche has extensive experience in oncology, particularly since they own Foundation Medicine. This suggests that Roche is happy with a two pronged strategy in oncology diagnostics, selling assays on their own through the partnership while their Foundation arm offers an all-in service.   But it also stirs the tea leaves in the genomics M&A pot.

JPM20: Illumina Launches Super Resolution Instruments

Illumina presented this morning at the J.P. Morgan Healthcare Conference (presentation, slides & breakout).  For us sequencing geeks, the biggest news is the launch of a pair of new sequencers -- but not where either myself or Shawn Baker anticipated.  Rather than doing something about the low end of their line (as I predicted) or replacing the MiSeq as Shawn guessed, Illumina perceived a need for desktop instruments to span the range between the existing NextSeq 550 and the NovaSeq and has christened the new instruments NextSeq 1000 and NextSeq 2000.  They also come with some slick new technologies embedded.

Is Illumina Vulnerable At The Bottom?

According to both the FTC and CMA, Illumina holds a nearly complete monopoly on the sequencing market, with other players (Ion Torrent, Oxford Nanopore) holding on to toehold niches.  Illumina has held that position for an extended period, so what might upset it?  I'm going to explore the case that they may have some serious inroads at the bottom of their line.

Might Illumina Shave NovaSeq Run Times?

I've had some people asking, either privately or via Twitter, what might come from Illumina next week at JP Morgan (8:30 am PST on Monday).  I have another post in the works (ideally going out not long after this one) on one aspect of their business, but then I thought of something else.  Something in the great tradition of proposing a plan while being quite unaware of all the critical details that the plan relies on!

A Le Mans for Clinical Genomics?

If you haven't seen Ford v Ferrari (or Le Mans '66 in parts of Europe), I strongly suggest you do so if it is still in a local theater.  I'm neither a gearhead nor a fan of watching automobile races, but while the movie is centered on an attempt to win the  1966 24 Hours at Le Mans, there is so much more going on.  Designer Carroll Shelby (Matt Damon) must not only project manage a difficult task, but also deal with unreliable allies (as one wag put it, the biggest villain in the title isn't Ferrari) and a cantankerous star driver named Ken Miles (Christian Bale).  One touching aspect of the movie is the portrayal of Miles' relationship with his young son, an audience proxy who idolizes but sees all sides of his father.  

Illumina & PacBio Throw In The Towel

I had planned to post this morning a "preview of 2020" piece I had drafted in my head on the ski slopes the previous two days, but never got around to actually committing it to bits and bytes.  Today's announcement that the Pacific Biosciences acquisition from Illumina is officially dead means the first item of that piece is mostly going uncaptured.

Long Overdue and Overly Short Notes on Clive's NCM 2019 Talk

A theme of the 2019 Nanopore Community Meeting in New York was the long and short of nanopore sequencing.  While the public sparring with Illumina/PacBio over the definitions of sequencing types wasn't explicitly discussed, certainly ONT wants to make sure that people understand they don't intend to ignore applications that are naturally short reads.  I've been slowly trying to get this summary to gel for awhile, with the usual distractions this time of year of some trips, planning for holidays and a bout with a virus.  Plus general procrastination. 

I'm just going to cover Clive's talk; there were some really spectacular presentations (including one by someone who remarked that they hoped their upcoming thesis committee meeting would go well! One of multiple excellent platform talks by very junior scientists) If you'd like to watch yourself, the video of Clive's talk is online. Watching it again is kind of fun, except for the distraction of seeing a guy with huge glasses trying to live tweet from the front row.  I've put in brackets rough timepoints for some of the topics; you may need to slide back or forth a bit to nail it exactly but they can land you near the right spot.

Merger Questions to Mull Over Your Cider

With the full FTC complaint against the Illumina-PacBio merger now out in the open but the holiday break bearing down like a reindeer on steroids, I want to leave you with a few questions to ponder over your wassail.  Because what holiday gathering is not enlightened by discussion on the Herfindahl-Hirschmann Index (HHI)?

FTC Slams Illumina-PacBio Merger, but Illumina Not Quitting Yet

Tonight I was intending to finally get out my summary of technical notes from the Oxford Nanopore Community Meeting, but yesterday the U.S. Federal Trade Commission issued a press release that they believe the proposed acquisition of Pacific Biosciences by Illumina would be grossly anticompetitive and cannot be approved in any form.  A more detailed report is promised but hasn't surfaced yet.  Curiously, not only did this ultimately move PacBio's stock very little, but today Illumina and Pacific Biosciences filed matching SEC documents that Illumina will continue to infuse cash into PacBio through March of next year.  Also, I should note that someone left a passionate defense of regulators in the comments on a prior piece, noting that the FTC decision shows that the CMA was justified in opposing the deal and not simply acting with a parochial eye on Oxford Nanopore.

Is ONT Really Going to Twist the Watch Stem Backwards?

I was in New York last week for the Nanopore Community Meeting.  I'll save some technical updates for tomorrow, for I wanted to focus today on a huge inflection point that Oxford Nanopore announced that they will really will punch through next year.  I'm going to do that with an extended comparison to Robert Bloch's wonderful short story That Hellbound Train.  I won't spoil that story, but if you want to first go find a copy to read (there is apparently now a graphic novel version) or spend a half hour on a decent narration of it, please do.  It's especially a joy if you're steeped in the lore of American railroading.

Should Patent Pool Save the ILMN-PACB Merger? ONT Doesn't Think So

Last week the UK’s CMA published a proposal submitted by Illumina and PacBio to save their merger. This was then published in a revised, seemingly more generous form on Wednesday.  Most strikingly, the proposal tackles head-on an elephant long in the room: is the CMA playing hardball because the biggest competitor in this space is not named Oslo Nanopore Technologies.

Genapsys Launches

Today Genapsys launches their sequencer into the U.S. market, with worldwide launch next year.  They also received a new round ($90M) of financing from a major firm, Foresite Capital.  In addition to the Press Release and Media Kit, Genapsys' PR team, provided me with answers to a set of questions I provided.  As a reminder, I previously covered their pre-print pushed out to BioRxiv six months ago.

CMA Drops the (Preliminary) Hammer on ILMN-PacBio

Today the United Kingdom's Competition and Merger Authority (CMA) issued their preliminary report on the proposed acquisition of Pacific Biosciences by Illumina.  The report has no dry British phrasing: they clearly state that the merger is anticompetitive and that the only legal remedy is to block the transaction.  Interestingly, today was also the scheduled Illumina Q3 earnings call, but the subject wasn't even broached there.

QIAGEN Quashes GeneReader

Two weeks ago QIAGEN announced they will discontinue development of their GeneReader short read instrument and move their portfolio of gene panel tests over to the Illumina MiSeq and NextSeq. Existing instrument owners will continue to be supported for an indefinite period.  Thus ends QIAGEN's effort to build a fully vertically integrated sample-to-answer diagnostic sequencing system, just short of 4 years from the system's launch. What can be learned from this and how does this reshape the sequencing market?

Illumina Throws PacBio An Extension and a Lifeline

Interesting news today on the PacBio front: as reported by GenomeWeb, Illumina announced that their walkaway date for the acquisition has been extended to March 31 of next year and that Illumina will be pumping significant cash into PacBio until either the merger occurs or is terminated.  In addition to publicly reinforcing Illumina's determination to get the deal done, the terms of the arrangement have interesting consequences should the deal fall through

Where U.K.'s CMA Missed the Plot

I've written far more than I expected to on the PacBio merger, with it dominating my output here this summer save that recent dip in the CCS boomerangs.  We still haven't heard from the U.S. FTC, which is the big hammer that could drop and the stock is still selling at a substantial discount to the price offered by Illumina.  While I've hinted at it, I've never quite detailed my major objection to the form of the UK CMA's analysis of the proposed acquisition.  I've missed the opportunity to lay that out during the period of public comment for the next round of the CMA.  Still, worth it to write it down.  Which was true about a month ago when I wrote this, then failed to actually push it to a post before I headed out for a rugged vacation in the American West.  And then forgot about it after returning.  And more news today to comment on -- so better finally get this out there.

Amazon Needs Another Training Track

I spent a day recently taking Amazon's "AWS Technical Essentials" course.  I had originally opted not to go, but a summons went out that we had already paid for seats and that everyone using AWS should really go.  I've been in far worse courses and certainly had no complaints with our instructor, a former mechanical engineer who knew his stuff and was never in salesman mode.  Indeed, many of the tips I extracted had to do with how to save money.  No, the problem is that the course is designed for a very, very different use case than anyone in my shoes is interested in.  It's a use case that I'm sure Amazon has a few bazillion customers for, but I'm just not one of them.

Mirror, Mirror Have You Leads, On My Strange HiFi Reads?

A core purpose of this space is to explore the current state of genomics technology.  Much of the time this is via distilling news reports, press releases and interviews with persons in the field.  But even more fun is to dive into actual data.  Such data is often accessed via the generosity of researchers who deposit open access datasets.  But it is also true that part of my professional responsibilities is to determine when new technologies and methods have applications at my day job, so I'm also charged in the day job with contemplating experiments to plumb sequencing systems.  Only by doing so can we ensure that we maximize our ability to perform cutting-edge synthetic biology.  A recent such experiment generated some curious data which I have obtained permission to share a subset of it publicly, as I'm scratching my head and hope that someone out in the community has insight.

Wall Street Bets Illumina Won't Acquire PacBio

The proposed PacBio-ILMN Merger remains an interesting spectator sport, with the UK's CMA looking for public input for the next round.  I don't usually pay attention to stock prices, but PacBio's current state presents too juicy a situations.  Just to be clear though: I do not hold any individual stock position in PacBio or Illumina (the bulk of my investing is in broad mutual funds, some of which certainly have bits of these companies).

UK CMA & ILMN/PACB: The Inconvenience of Being Earnest.

As part two of a yet-to-be-determined number of pieces on the UK's CMA preliminary analysis of the proposed Pacific Biosciences acquisition by Illumina, I'd like to briefly explore the surprising authority of this agency to plumb internal documents at the two companies.

UK CMA's Write-up of PacBio Acquisition by Illumina Makes for XXX Reading; Clearly They Believe XXX and XXX

After writing my two recent pieces on the business side of the long read industry I planned, after a recent extended family vacation, to try to get back to science.  Particularly after my chagrin when various correspondents pointed out a fact from each I should have found and didn't: in my ONT piece I failed to discover that ONT has two share classes and the Woodford fund's shares cannot be used to gain control of the company and in the PacBio piece that there is a $100M breakup fee due PacBio if for any reason the deal doesn't go thru.  I'm particularly red faced on that one, as a breakup fee would play importantly into PacBio's financial health should the deal go south; $100M would buy perhaps two quarters time.

But then a bunch of people threw my way the UK Competition and Mergers Authority (CMA) report on the merger and I foolishly opened the document.  It makes for interesting reading, but that is hampered by the fact it is highly redacted -- like my title. Reserving the right to comment on the contents substance at a future date (or never), I'd just like to give a tour around some of the redactions.

Will Regulators Scotch PacBio Acquisition?

When Illumina announced its proposed acquisition of Pacific Biosciences last fall, an immediate question arose as to whether the deal would pass antitrust review.  Illumina must have been optimistic, as they originally expected the deal to close in "mid-2019".  That timetable has now been rolled back to late 2019 in the face of the UK agency with jurisdiction over mergers deciding to go for a second round of review and no word yet from the U.S.'s Federal Trade Commission.

ONT & The Woodford Liquidity Squeeze

There's an unfortunate chain of events that may end up causing a headache for Oxford Nanopore, and it's completely outside their control.  One of the their key investors has just had his luck - or perhaps more critically his reputation -- at stock picking disintegrate.  Because of some unusual choices, that has potential repercussions for ONT.

The Genius of Plongle

I noted in my roundup of Oxford Nanopore technical announcements that I loved the Plongle concept.  This is really both a new application-specific integrated circuit (ASIC) and using it to build a 96-well sequencer.  Let me expand on what there is to love.

ONT's Horrid Data Storage Folly

In the coverage of ONT's announcements at London Calling, I specifically left out one of Clive's Skunk Works projects.  This would be a device to use nanopores to write digital information.  I'll give him points for creativity, but the reason I held this for here is I truly and sincerely hate the concept and didn't want my vitriol to distract within the other piece.  But here I will let loose.

ONT's London Calling Announcements, Pass One

The annual big Clive Brown London Calling talk had a twist this year  Brown introduced a set of senior lieutenants at Oxford Nanopore and then tacked on a few "and one more thing" moments at the end.  If you're looking for the TL;DR version from me, it is that there were a lot of sensible but non-Earth shattering updates from the team followed by Clive updating on one prior crazy idea and throwing out two more -- one of which I love and the other I believe should be thrown out posthaste.

Nanopore's Long DNA Paradox

The first half day of London Calling has already delivered the usual mix of scientific excitement.  The prospect of lives, particularly those of children, en masse by delivering precision oncology broadly across sub-Saharan Africa.  Dizzying levels of alternative splicing in a key brain ion channel.  RNA modifications in great numbers.  That one was also gratifying as it was commented that even without a basecaller, modified bases can be be suggested by higher error rates around a particular motif.  Around 2015 or so I noted in the Nanopore Community post that error rates went up around GATC sites in E.coli, the target of Dam methylase.  Protein tags read by the current nanopore scheme. Tonight we get Clive and company performing their usual razzle-dazzle of product announcements; one person pointed out to me a possible angle I failed to include in my laundry list is the raising of the speed limit from 450 to perhaps 1000 bases per second.  But another omission was front-and-center in the plant genomics sub-session I attended and could be called the central paradox of the current state of nanopore sequencing:  pores are great for long DNA but long DNA is not great for pores.

Care to Pore Over My Laundry List?

London Calling is this week, so get ready for lots of Oxford Nanopore in my Twitter channel and if I'm on the ball, in this space.  ONT has made a number of releases and updates and there have been other developments within the nanopore ecosystem which I've failed to report.  Here, in not terribly organized fashion, is a laundry list of things I'm thinking about going into the meeting

Mass Recoded E.coli Genome Not Tripped Up By Programmed Frameshifts

There's a paper this week in Nature announcing an E.coli genome which has had two serine codons (UCA, UCG) and one stop codon (UAG) removed from usage.  It's a major work on synthetic biology and represents the largest designed sequence ever built.  In contrast to Craig Venter's early effort, which moved a synthesized genome into a cellular ghost of a natural bacterium, this one replaced the native E.coli genome in stages -- Escherichia theseusshipii would be a good name for the new strain. But is the genome quite what is advertised? Following up on a pair posts from Sandeep Chakraborty showing remaining UCA, UCG codons and UAG codons in a bunch of typical genes, I decided to look for a trickier set of possibilities to overloop -- and by luck or care the Nature paper got these.  Just to put one gripe front-and-center, the group deposited in Genbank the reduced genome version of E.coli they started with, but not the recoded genome, which is in the supplementary material

My Career's Double Slit Experiment (or, A Funny Thing Happened on the Way to the Drydock)

When I announced recently that I had moved over to Ginkgo Bioworks, I was compelled to leave out an important part of that story.  Indeed, by just focusing on the (still open) position of NGS Head, I could avoid the sticky subject of how exactly I ended up there.  Today the press release finally went out and the fact that Warp Drive's genome mining business is now owned by Ginkgo is public (covered nicely by Amy Feldman in Forbes).  But in the spirit of my periodic public coverage of my own journey, here is some of the rest of the story.

Genapsys' Base Caller: Mysterious, But Not Ideal?

When I wrote about Genapsys' pre-print on their sequencing system the other night, I intended that to be the last I wrote until some major news from them.  But after launching that into the great Internet ether,  I found myself lying awake wondering if a very simple idea had any merit.  Painfully simple -- I almost didn't pursue it because it was so simple and obvious.  But, it turns out it appears to have merit -- there may be an obvious route to improving the accuracy of Genapsys' basecalling on homopolymers.  And that also took me into ground I've thought about before -- going back to my first year at Codon Devices over a decade ago -- on the challenge of modeling sequence quality.

Poking at Genapsys Preprint

Genapsys is continuing down the path of pre-launch information, most recently releasing a pre-print.  I'm looking at this pre-print critically and unfortunately turning into a bit of Reviewer #3.  Not that anything is fatal and pre-publication review is a key value to pre-prints. If I were an actual reviewer I'd be writing mostly the same things and covering more vertebrate species than they sequenced (a human exome panel  was included, though most samples were bacterial) -- I'd grouse about a missing figure (which I've provided), carp about critical details not provided and beef over a public data deposit that doesn't really line up with the unqualified claim made in the paper. (*)

Want to Run An Exciting Sequencing Group? Ginkgo Is Looking for You!

I've awakened from my blogging torpor to point out a really interesting career opportunity for the types who might read this space. Ginkgo Bioworks, one of the leading synthetic biology companies in the world, is looking for someone to run their existing Next Generation Sequencing group. It's a chance to run an energetic high-throughput sequencing group that works on a wide range of projects. And, as you might of guessed from the fact I'm writing about it here, you'd also get to be my boss. I'm hoping many will see that as a feature and not a bug.

Nanosens Publishes Proof-of-Concept for Point-of-Care CNV Diagnostic

Here's a killer technological challenge for anyone: design a scheme to detect vanishingly small concentrations of a valuable analyte in a biological fluid.  The assay must require zero pipetting, work in the field at ambient temperature, generate results quickly, contain positive and negative controls, be usefully precise and accurate, and be usable by personnel with no formal technical training.  Oh, and be dirt cheap as well.

Beyond Generations: My Vocabulary for Sequencing Tech

Many writers have attempted to divide Next Generation Sequencing into Second Generation Sequencing and Third Generation Sequencing.  Personally, I think it isn't helpful and just confuses matters.  I'm not the biggest fan of Next Generation Sequencing (NGS) to start with, as like "post-modern architecture" (or heck, "modern architecture") it isn't future-proofed.  Not that I wouldn't take a job with NGS in the title, but still not a favorite.  High Throughput Sequencing feels a little better, but again doesn't leave room for distinguishing growth -- and HTS as an abbreviation is already going to confuse anyone in Biopharma who thinks about High Throughput Screening.  Massively Parallel Sequencing sort of works, but my late father had a real pedantic objection to using "massive" for anything that lacked mass, and while I don't subscribe to that view such uses just don't sit well with me.  Worse, as I'll explain, trying to divide sequencer technologies into Second and Third generations creates more heat and smoke than light.  On a number of Twitter threads I've tried to launch my own terminology, but probably haven't been terribly consistent.  So here is an attempt at that.

Failing to Fetch An Interesting Result on Dog Oncogene Homologs

An idea for a little exploration occurred to me back at Infinity -- that is 7.5 years ago -- that I've never tried out.  But I never got around to it.  I had some downtime recently  to play around so I finally executed the experiment -- alas, it turns out not to be very interesting.  Still, a negative result is a negative result.

Covaris Grabs A Spot on the Liquid Handler Deck

For as long as I can remember, Covaris has been the standard in DNA shearing for high throughput short read sequencing.  Their benchtop units had their quirks -- custom tubes being the foremost -- but they were what everyone else compared to.  In 2013 when the American Society for Human Genetics was in town, the PacBio folks did me a great favor and loaned me an exhibit hall pass.  Multiple companies were offering DNA shearing instruments -- and every one compared themselves against Covaris.  Now they have a new offering, moving the instrument onto a liquid handling robot deck so that it is available for high-throughput workflows.  Covaris invited me down to their Woburn, Massachusetts facility to get a look at the instrument before its formal launch at the SLAS conference

Patent Dive: Genapsys

Here's a dangerous statement for me: I actually enjoyed reading some patents recently.  Now, before you get any ideas in your head about suggesting more patents for me to read, let me be clear that these were unusual patents -- they're written to be read! -- and were read under strict conditions. The patents in question are from Genapsys -- found via my good friend Justia.

Metabolic Whac-a-Mole

Derek Lowe summarized a really cool paper back in October.  I've been meaning to grab a copy, but discovered recently that the MIT library no longer has an easy way for outsiders to slip in an use their subscriptions.  So I'm working off his summary, but since this is mostly an excuse for flights of genetic fantasy actually reading the paper would probably just hinder me!

2019 Tech Speculations: Oxford Nanopore

As promised in the last post, I'm segregating out Oxford Nanopore.  Admittedly I tend to cover them relatively closely -- though I never seem to quite finish writing up their conferences -- but at the moment ONT is the only major player in the U.S. research sequencing market not being run out of (or about to be run out of) Illumina HQ.  And I'll be very to the point: ONT has a lot of balls in the air and irons in the fire, but from my point-of-view what matters most is rapid and regular progress on the accuracy front.

2019 Sequencing Tech Speculations: Will We Actually See New Entrants?

An astute reader caught a sentence fragment about MGI in last night's Illumina JPM roundup -- the unfortunate evidence of a a mental battle over whether to put any further comments on MGI in an Illumina-centric post. So now I'll sweep that bit into a general post about not-Illumina (and not-Oxford, that will go in yet another).

Illumina JPM Talk

Illumina CEO Francis deSouza delivered his J.P. Morgan Healthcare Conference talk (webcast audio, slides & Q&A audio) a week ago.  I can claim that some of my speculations came true -- just the most boring and obvious ones.  Overall, the presentation was the talk of a confident market leader.

2019 Sequencing Tech Speculations, Part I: Illumina & MGI

Next week is the J.P. Morgan Healthcare Conference.  It's striking this year the paucity of companies in the genomics space -- Illumina on Mondayat 6:00 EST and MGI on Wednesday at 5:30 EST and Nanostring at 6:30 EST on Wednesday.  Perhaps NVIDIA will say something interesting about their forays into healthcare, such as providing the chops for real time nanopore basecalling, on Thursday at 11:30 EST. There's also some nice polls from Albert Viella on Twitter

What would you like @illumina to announce at #JMP2019 ? https://t.co/TDn5J0glhi part 2

— Albert Vilella (@AlbertVilella) January 5, 2019

and some more Twitter speculation

Predictions for @Illumina #JPM2019. Besides PacBio news, expecting NovaSeq SP 2x250. Any longer S4 kit or potential S5 would require upgraded onboard storage. Really hoping no new NovaSeq system.

— CAT at UCSF (@CAT_UCSF) January 4, 2019

So, before all the beans are spilled, here's some of the speculations and ponderings I've been entertaining about the sequencing technology field for 2019 for Illumina and MGI.  I'll cover some of the other players in the next few days, but since Illumina is up on Monday that's the priority!

2019 Resolutions

2019 is upon us; I'm hoping it will be a bit less eventful than 2018.  It wasn't all bad -- I took two trips that delivered scenery I have only right to see once in a lifetime -- but it was essentially bookended by losing my father and a revolution in my workplace.  Mixed in there is the bittersweet pride of seeing one's offspring graduate from high school and proceed on to college.

New Year's resolutions are notoriously difficult to keep -- one is fighting entrenched behaviors -- but bringing in some external pressure might help.  So I'll make my two resolutions for the year very public: that I post here more regularly and that I read more non-fiction books to the end.  And the hope is that you, dear reader, if you meet me, feel free to pointedly inquire about my adherence.  Or hit me via Twitter!

An Unfortunate Master Class in Poor Plotting

I hope my admiration for Pacific Biosciences intellectual acumen was clear in my post on the acquisition by Illumina, because now I'm going to be a rabid crab over a webinar they aired yesterday.  I take telling scientific stories seriously and an important part of telling such stories is displaying data well.  I'm a perfectionist in this department by intention, but not always by execution -- I'm constantly reanalyzing my plots and diagrams for errors and cringing when I find them.  The webinar is trying to extol the value of the latest developments in the SMRT platform, but the data graphs often actively fight against any understanding or excitement.

Flappie vs. Albacore via Counterr

I'm going to go through some analysis of Oxford Nanopore basecalling, running some quick comparisons using a freely-available tool called counterr which was announced at the Nanopore Community Meeting two weeks ago.  Counterr was developed by Day Zero Diagnostics, a startup I advise -- though in announcing yet again my COI I will stress I don't get paid to help give away software!  This is just a small bit of analysis; nothing as comprehensive as Ryan Wick's ongoing analysis with a ready-to-submit preprint masquerading as a README file.

Nanopore Community Meeting 2018: The Clive Report

Given it's late and I just dashed through a classic San Francisco downpour, I'm going to mostly stick to covering Clive Brown's talk tonight.  Within it there were a number of announcements, and for anyone following this space I get to point out things I've proposed in the past that are moving to fruition as well as recent statements I made that were quite erroneous.

Also note that tweets during his talk have been collected by ONT into a Twitter Moment

A Few Things Before Nanopore Community Meeting Begins

Nanopore Community Meeting begins within the hour.  San Francisco is spectacular as ever -- Alcatraz Island disappearing into the fog as I fiddled with camera settings, the spectacular Bay Bridge spans are visible from the the breakfast area and I even got to see some notable locals on my walk over from the hotel

If this crowd doesn’t get a move on, they’re going to miss #nanoporeconf breakfast pic.twitter.com/rFwfGdQTit

— Keith Robison (@OmicsOmicsBlog) November 28, 2018

Hans Jansen was kind enough to remind me by tweet of a couple of missed topics in my preview piece.  So let's cover them!.

Nanopore Community Meeting 2018 Preview

Okay, now that I'm done venting -- for now -- about ONT's customer service experience  (well, almost done -- they sent me the same damn letter they sent my colleague -- why were they several hours apart???) -- let's move on to the Nanopore Community Meeting.  Technically it started today with the training session, but I'm not heading out until tonight.  At the first one of these in NYC Oxford tried to avoid making any announcements, but they seem to now like having two major focus times a year sometimes supplemented with Clive Brown webinars in between.  Here are some

How Not Do Think Like A Customer: Examples from ONT and AMZN

I'd planned today to use some downtime to write up a preview of the Nanopore Community Meeting which I am attending tomorrow and Thursday.  I might still do that, but the same organization just engaged in the sort of customer engagement that drives me batty (yeah, twisting the lion's tail before entering their den -- smart move or what?) and it reminded me of another lousy experience I had recently with a very prominent company: Amazon.

Failure: The Real Secret Sauce of Engineering

I took one swing at Vijay Pande's overly rosy piece on applying engineering methods to biology and medicine and similar minded efforts were published by Ash Jogalekar at Curious Wavefunction and Derek Lowe at In The Pipeline. Perhaps I shouldn't make another go, but it is a new excuse to explore an old fascination of mine.  Pande's subhead was "Billion-dollar bridges rarely fail -- whereas billion-dollar drug failures are routine".  I can't argue that.  Actually, it would seem from an informal search that billion dollar bridges are actually much rarer than billion dollar drug development programs.  Obviously they exist -- I've traversed the new Tappan Zee Bridge which came in over $3B.  On the other hand, a second crossing at perhaps the most notorious spot in bridge engineering history, the Tacoma Narrows, was built earlier in this century for only $0.8B.  What I wish to explore are the failures of bridges and other structures of any cost, as it is the analysis of failures that frequently propels engineering forwards.  That analysis is enabled by the relative simplicity of human engineering and the artifacts it uses and creates.  Conversely, analyzing the failure of new drugs is nothing like that.

No, the Groves Fallacy Can't be Retired Yet

Vijay Pande has a thought-provoking piece in Scientific American on the Groves Fallacy, though in the end I'm afraid mostly what he provokes in me is the thought that he's in most cases pretty far off base. Titled "How to Engineer Biology", he claims that the Grove Fallacy -- the idea that biology can't be tamed by engineering -- is quickly being put to rest.  And Pande isn't some naive Silicon Valley type, but a professor at Stanford whose lab works in experimental biology.  So he has some street cred -- but that doesn't mean he isn't mostly wrong.

Illumina Buys PacBio: More Thoughts

Illumina surprised pretty much everyone in the genomics community by announcing the purchase of Pacific Biosciences.  I had spent Thursday deep in the weeds of a combined PacBio-ONT-Illumina dataset, so was caught completely by surprise on my commute home by an email asking for my comment.  If you do want to hear hot takes on it from myself and AllSeq's Shawn Baker, Theral Timpson over at Mendelspod interviewed us that night.  There has of course been much discussion of the deal and tributes.   I've had the weekend to ponder things, and here are some somewhat better thought out and detailed comments -- though I don't believe I've retreated from any of the themes in the podcast.  I've grouped the thoughts into a few themes.

You Can Be Impatient Running MInIONs, But Not Feeding Them

Yes, it's been way too long since I wrote here.  Even longer since I did so with any regularity.  There was always some list of things draining my time and energy.  But I resolved this week to get back on the horse -- and that was even before today's bit of dilithium news. In particular, in one twenty-four hour span three different people remarked on the prolonged hiatus -- a professional contact, a commenter on the blog and finally some very cutting remarks from Draco (aka TNG).  And what better way to get going again but to kvetch about Oxford Nanopore's supply chain model?

Two Museums Guaranteed to Fluor You

I've been horribly neglecting this space for an extended period.  Contributors to that include a TNG eclosing from high school, ferrying grandparents, a milestone (or is it millstone?) birthday and a 10 day vacation with poor Internet service.  Oh yeah, another one of those starts Thursday.  Then there's keeping the genome factory going -- at times I feel like a worker in Fritz Lang's Metropolis.  But someone even noticed and emailed me today whether this hiatus would end, which is beyond reason enough to get going.  But tonight's entry has nothing really to do with biology or genomics, but rather hearkens back to the first science I fell for.

LC2018: VolTRAX

In my preview ahead of London Calling, I suggested that VolTRAX is a device that still hasn't found its raison d'etre.  With the meeting, the device officially pre-launched and the company is now taking pre-orders for delivery in the Fall.  And it still feels like a device which hasn't yet found its purpose, though Clive Brown presented a dazzling (if perhaps distant) vision of where VolTRAX might go.

LC2018: Flongle, Ubik-a-something and Metricoin

London Calling has been over for nearly three weeks.  I originally wanted to write up at least something after the first night, but fatigue overcame me and I didn't get anything useful put together.  And then travel and more fatigue set in.  But beyond that and the usual temptation to procrastinate, there is the challenge of forming a coherent narrative from all the different threads at the meeting.  There's all the Oxford Nanopore official announcements and then various user presentation tidbits.  After several failed mental attempts to compose a big picture take on everything, I've decided to try to write a series (number yet indeterminate) of posts that will focus of various axes of the meeting.  Hopefully they won't be to redundant -- or self-contradictory -- and that by following one particular thread I can actually condense some coherent thoughts.  This first such thread starts with Flongle.

Miscellaneous & Disorderly Thoughts on the Eve of London Calling

It's the night before London Calling. I hope to post Thursday, but an after-meeting report won’t be until nest week - I must dash on Friday fir a slightly insane/exhilarating routing to meet my family in Florida for the holiday weekend. Exhilarating as I will have a layover in one of the ancient capitals of Europe, Lisbon, which I’ve never visited. Insane, because it’s a 12 hour overnight layover. Anyway, between the challenge of covering Oxford Nanopore's expanding reach of products and applications and being sleep-addled from taking the redeye flight I'm going to throw out a bunch of thoughts without really trying to fuse them into a coherent narrative.

Should PentaSaturn Buy An iSeq: A Hypothetical Scenario Illustrating Platform Picking

Editorial note: I wrote this in early January, then planned to slot it in after some other items.  Then life knocked me upside the head, then AGBT came along and then it was forgotten.  Once I remember it, I fretted it had gone stale. But I had put a lot of effort into it and really nothing has changed with regard to iSeq, other than it should be shipping now.  Besides, this week is London Calling and so having an Illumina-centric piece could be a bit of useful balance.  So, for your consideration:

Some of the online discussion around this January's iSeq announcement, springing from my piece or elsewhere, explores how the iSeq fits into the sequencing landscape.  In particular, how does it fit in with Illumina's existing MiniSeq and MiSeq and how does it go against Oxford Nanopore's MinION.  For example, in Matthew Herper's Forbes piece, genomics maven Elaine Mardis compares iSeq unfavorably to MiSeq in terms of cost-per-basepair.  I'm a huge believer in fitting sequencing to ones scientific and practical realities and not the other way 'round: no one platform quite fits all situations nor do even the same metrics fit all situations.  So in this piece, I'm going to illustrate what I believe is a plausible scenario in which iSeq would make sense.  Now, I have designed this to play to iSeq's characteristics and very realistically have many dials which I could turn to go in another direction.  Which I will try to note as I go along.

PromethION Racing: A Call To The Post

I was at a get-together yesterday for bioinformatics folks associated with Third Rock Ventures companies at a local pub.  The organizer, who I've known for a number of years, was introducing me with the pleasant "Keith writes a nice blog" -- but then the barb "but he hasn't posted in a while". Ouch! But it hurts because it's true; too many excuses to not write and far too many half-baked ideas and interviews that should be out (or worse, a nearly complete post).  Since it is May, which in the U.S. is bookended by iconic racing events, I'd like to trot out an idea that has been idling for a while: PromethION Racing.

Mission Bio Launches Custom Panels

Back in October I covered the launch of Mission Bio's single cell platform, Tapestri.  Tapestri is a microfluidic platform which encapsulates cells and sets of barcoded primers into droplets, lyses the cells within the droplets and executes PCR on the released DNA.  Mission initially targeted hematologic cells, since they do not require disaggregation, and offered a standard panel of primes.  Around the time of AGBT, Mission launched a custom panel option and took the time to sit down with me.  Now with AACR, Mission has announced placing Tapestri at multiple major cancer centers: the NCI, Mt. Sinai, MD Anderson, Memorial Sloan Kettering, St. Jude's, UCSF, U Penn and Washington University.

A Small Rampage Over STAT's Movie Piece

A movie opened this weekend which, by all prior evidence and new reviews, is unbelievably silly but destined to rake in the bucks. Rampage is very loosely - as if it could be another way - based on a video arcade game. The original game’s backstory had a mysterious ray transforming people into monsters, but the movie has changed that to CRISPR. So STAT had a piece which, to my great disappointment, gave the movie’s science a near pass in a piece featuring two writers chatting . . (Note: this post has mild spoilers, though if you've seen the trailers they give almost all of this away).

A Most Unfortunate Sequencing Error

If you are in the sequencing business, you'd like to get things right.  But sequencing is a form of measurement and measurement has error.  No matter how diligent and committed you are, sometimes the data doesn't break your way.  Mick Watson has a set of posts and a preprint illustrating quality issues in many deposited bacterial genomes.  Some of those are bad luck and some of those are from complacency.  Some errors radically affect biological interpretation and some don't. I'm going to detail here one of the worst cases of bad luck I've seen, where relatively small errors sat undetected for over a decade and triggered some published head scratching over their erroneous implications. So let's look at the rap sheet of this error.

A Morning Visit to SeqLL

I've written in the past about SeqLL, the company which purchased all of the hard assets from Helicos after the latter's demise.  At the end of last year, CEO Elizabeth Reczek invited me to stop by for a visit and so I spent a morning having a frank discussion with Dr. Reczek and Director of Sales Lee Dalton and also was treated to a tour of their facilities.

PromethION: Straining at the Starting Gate

Due to the usual time conflicts, I've only watched bits-and-pieces of the Winter Olympics from South Korea. Which is unfortunate, as I do enjoy observing many of these events as so many combine grace, power and finesse.  In the various timed events, the competitors can be seen tightly wound, ready to spring out at the crack of the start.  Increasingly, that is how Oxford Nanopore's PromethION looks: a superb performer ready to bolt away.

AGBT: It Ain't Over 'til the Tattoo Wears Off

AGBT officially ended on Thursday night with a space-themed party, but I have a bunch of notes from interviews with company representatives and even a few notes from sessions.  So be prepared for a string of further AGBT reports.  This dispatch will have some overall thoughts as well as some notes on the possible return of AGBT to Marco Island next year.  I also want to mention two good AGBT 2018 summaries, one from Dale Yuzuki and another from Decibio's Stephane Budel.

newly applied

AGBT: BioNano Launches New Labeling Approach

AS AGBT opened, optical mapping company BioNano Genomics announced a new scheme for labeling genomic DNA inputs which substantially improves performance.  Sven Bocklandt from the company sat down with me yesterday to walk through the new Direct Labeling

AGBT: Twist Biosciences Launches Sequence Capture Product

Twist Biosciences today launched a new product into the sequence capture space.  CEO Emily Leproust was presenting to the Gold Sponsor workshop as I started writing this, but she also sat down with me yesterday to preview the new offering for targeted sequencing.

AGBT: 10X Previews Three New Single Cell Applications

I spent breakfast with 10X Genomic's Michael Schnall-Levin and two of his 10X colleagues gave me a sneak peak at three new single cell products they are rolling out at the workshop I'm typing away at now.  These enable measuring protein targets of antibodies, mapping out accessible chromatin regions with ATAC-Seq, and mapping copy number variants (CNVs) at single cell resolution.  All use the existing Chromium Controller instrument.

AGBT Swag Bag

Today at AGBT is light on the science talks; the afternoon is free for lazing around the resort complex -- or for swimming laps in the lazy river (which makes it a not-so-lazy-river). I can only manage downstream; upstream is an aquatic treadmill.  A key task on Day 1 is to pick up one's registration materials.  At one conference I failed to do this promptly and discovered to my dismay that the desk wasn't open during the opening reception slash poster session -- so despite being a speaker I had to sneak into the room via a side door!  Registering means picking one's meal pass -- I took the temporary tattoo over the wristband option -- and grabbing the vaunted AGBT backpack.

AGBT 2018: It's Great to Be Back

All sorts of scheduling snafus have kept me away the past three years. So this time around, I vowed to go and made sure my calendar stayed clear. So clear, I forgot to put a reminder down to actually register for the event. Luckily, there were slots still available when I put my flier in.

Brown Webcast Note: Corrections and Expansions

After I post something, there's almost always something I realize I left out.  In my piece on Clive Brown's webcast of ONT improvements, not only did I forget a few key details but my wording led to some unfortunate confusion, as judged by a comment.  Someone took me up on my idea on how detecting large fragments during a run might work -- and showed it doesn't pan out (which Clive Brown confirmed).  And to top things off, a BioRxiv preprint showed up that exactly covered something I alluded to.

February 2018 Clive Brown Webcast Notes

Clive Brown's webcasts are always entertaining, and even the 6am Eastern Time start for Thursday's didn't hinder that aspect -- though I am thankful I'm not on the U.S. West Coast because I really don't function at 4am.  Even at 6am, I was frequently shutting off my iPad screen or exiting the presentation, as screenshots on iOS involve simultaneously pressing Power and Home keys.  At that hour, my never great fine motor skills just aren't reliable.  Hopefully I won't make the dog's breakfast of this, as that's usually all I'm good for processing at that hour!

Still, lots of updates and promises as well as a number of "wait until London Calling" teasers.  Just to get this out of the way, I'm going to report the launch dates that Oxford mentioned -- anyone in this space should know that Oxford is very good at delivering what they promise, but not very good at delivering when they promise.  You can also find notes by David Eccles to check me against or watch the presentation recording from ONT.

Oxford Nanopore Outlook 2018

I'm behind on these posts.  My usual foibles were largely responsible for a while, but then I had the major (and sad) family issue that has kept me off balance for  two weeks. Someday I may write about that, but for now back to the major sequencing vendors.  Though with Oxford Nanopore, the problem is where to start?  But now is the time to get moving, both since Oxford's Clive Brown will be webcasting an update on Thursday and I'll be at AGBT next week and expect to be busy with news flow from that event. Clive's webcast is titled "sub-$1000 human genomes on Nanopore (and other goodies for H1 2018), so expect quite a casserole of tempting updates.  Certainly it is enough to get me to try to be fully mentally awake at 6 am, something that does not come naturally.

Fingerprints on Jupiter

I had hoped to mark my father's 93rd birthday today in my usual way, a call home to exchange well wishes and update him on our goings-on.  But two weeks ago he entered the hospital for what turned out to be a final visit, so instead I am writing this.

PacBio Outlook 2018

Well, I didn't exactly get my Pacific Biosciences preview out before their J.P. Morgan presentation.  Luckily, the slides for that primarily projected financials and touted their successes -- and didn't drop any major platform announcements in -- so I didn't miss out.  PacBio's position is important and worth reviewing, even if it doesn't change much.

iSeq!

Illumina CEO Francis deSouza's J.P. Morgan Presentation did not disappoint.  While humdrum financials and touting market dominance and areas of future growth came first, then came the big Firefly announcement (with a name change to iSeq 100)  -- and then after another short spell of reviewing the latest Nextera chemistry came a smaller bombshell -- Illumina is partnering with former arch-rival Thermo Fisher (nee Life Technologies nee Applied Biosystems) to move the AmpliSeq multiplex PCR technology over to the Illumina platform.

Illumina Outlook II: The Fleet

In my prior installment I looked at Firefly, now clearly a working instrument.  Now I'll take a peak at the rest of the Illumina fleet.

Illumina 2018 Preview I: Firefly

Time to start gazing into my cloudy liquid crystal ball and attempt to see what will happen in the sequencing world in 2018.  J.P. Morgan is next week, which puts a time box on getting predictions out. One thing I see on both my personal and blogging horizon are flying creatures bearing light.  On the local front, TNG has decided to head this fall to the City of Brotherly Love to learn to fly and breath flame.  But in the sequencing world -- well, I'm going to need to pack a huge Ball jar for my trip to AGBT this year, as I plan to hunt out a Firefly.

Remembering 2017's Losses

A new year beckons and with it a burst of enthusiasm for writing.  Which also means combing through post ideas from last year that never quite were completed -- some as stubs or at least headlines.  But before tackling the new, I feel I need to tackle some personal losses in 2017.

2017 Nanopore Community Meeting: An Incomplete Summary

The 2017 Nanopore Community Meeting was over a week ago back in New York City, so I'm grossly overdue in cobbling together some observations and opinion based on the tweet stream (I had a critical day job meeting at the same time and wasn't in New York).  I did dash off the bit about SmidgION being potentially like the early Macs (though I got wrong the nomenclature, the original was the Mac 128K -- Mac Classic was a later model that resembled it).  Oxford also deviated this autumn from the pattern of public information they had seemingly established, with major news at London Calling and smaller updates at the community meeting but also a pair of Clive Brown webcasts each falling roughly halfway between the two meetings.  This fall, no webcast.

Nanopore's have their own Day 1 and Day 2 writeups and an independent write-up from Arwyn Edwards.

Platform

Per the usual pattern, Oxford showed off previously announced hardware but made no solid announcements.  I've put together a Storify of relevant tweets which may hold further information.

Flongle/SmidgION

SmidgION pumping out data with an attached Android phone calling the bases was a heavily tweeted and retweeted photo.  Alas, Oxford apparently put release of the SmidgION/Flongle components into the second half of next year, so no SmidgIONs adorning Christmas trees this year while happy recipients sing Flongle Bells ("Oh what fun, it is to sequence, in a one horse open sleigh, hey!").

Anxiously waiting for these little bad boys to develop! SmidgION for sequencing w cell phone connection & Flongle, reduced version of a flow cell #nanoporeconf pic.twitter.com/2xsQOKPVle

— Aaron Pomerantz (@AaronPomerantz) November 30, 2017

Seriously, as suggested by the previous post I think these smaller flowcells are going to be hugely popular and influential.  For training and educational purposes, small is better.  The targeted application of field operations will be huge.  

But I think in the end the biggest use will be for many applications in which there are large numbers of samples from which small amounts of data will answer the scientific question and where multiplexing isn't a good solution.

To give one example, there is one of the burning questions of DNA sample prep: what contaminants damage flow cell performance?  Obviously that isn't a question suitable for multiplexing!

But there will be many others, particularly for counting applications.  Especially if "no library" approaches are developed along the lines suggested previously by ONT for their Cas9-based schemes.  If creating a sequencer-ready sample consists of just pipeting a small amount of inexpensive reagent, then a lot of new applications will open up.

GridION

No real news specifically about GridION X5, other than that many people have tweeted out pictures of their new GridION instruments and there have been very few reports of problems (I know of at least one example of one being dead-on-arrival, but that seems to be rare).  

But the big news tied to GridION is the launch of the first two contract research nanopore sequencing services, with the Garvan Institute in Australia and BaseClear / Future Genomics Technologies in the Netherlands.  Since Oxford won't license MinION users for service sequencing, only the availability of GridION made this possible.  Presumably nailing down a U.S.-based operation is a priority for ONT; I've shipped samples overseas for sequencing but it is never a calm process plus it creates additional scheduling headaches (never, never let your samples sit around at a shipping firm over the weekend!).

PromethION

I wrote a very critical piece on PromethION last year.  The instrument isn't out of the woods yet, but 

Twitter traffic does suggest that Oxford is sending out small quantities of good flowcells.  Clive Brown tweeted that his yield from a PromethION flowcell is pushing what would be needed for 30X coverage of a human genome; of course Clive's yields are historically about 2X the best field yields and 3-4X better than what most users achieve.  So perhaps PromethION will be a real star of data production for London Calling 2018 presentations, but I certainly don't see that as a sure thing.

Basecaller Widget

ONT started showing off their prototype of the FPGA-powered stand-alone basecalling widget, also announcing a contest to name the device.  

Yet to be named basecaller dongle #fpga magic plug-in hardware. SmidgION for scale #nanoporeconf pic.twitter.com/PZgDpiEqX6

— Martin A. Smith (@martinalexsmith) November 30, 2017

VolTRAX

VolTRAX is still in the "VIP" beta test phase, which I am not part of.  I believe the only available kit is still the rapid 1D DNA kit, which hasn't attracted a fan base as the conventional protocol is so simple.  ONT promised version 2 flowcells which will have capabilities such as thermocycling.

Software

On the software side, Oxford touted their improved Scrappie basecaller and a new Tombo package for modified base analysis. You can find tweets on this and others related to base modification in a Storify.

I really can't do justice to Ryan Wick's talk -- if you want to get the latest on basecalling performance, check out the publication-ready README file from Ryan Wick which compares just about every known basecaller -- including the not-yet-public Guppie GPU caller -- on a variety of metrics.  Here's one example, showing raw basecalling accuracy.

Cold Chain

ONT has been making progress in reducing the cold chain requirements for select kits.  Flowcells are now being shipped wrapped in wool and they are beta-testing lyophilized versions of library prep reagents.  That would of course be huge for field use, but not inconsequential would be reducing the shipping costs for all users.  If you're going to be a low cost platform for hobbyists and educators, those shipping charges add up.

NanoBind

Not ONT, but a company called Circulomics announced plans for a sample preparation technology called NanoBind.  These are described as

a thermoplastic disk that contains a high density of micro- and nanostructured silica. This unique structure enables vast amounts of DNA to bind and release without being damaged. Processing occurs through a rapid bind, wash, and elute process that parallels magnetic beads and is easily automated.

Prep time is promised at 45 minutes and claimed to deliver up to milligrams of high quality, high purity HMW DNA from 1.5mL of input material

RNA

Probably the biggest splash of the meeting was the release of a large consortium RNA dataset for human cell line NA12878, with both 13 million direct RNA reads (from 30 flowcells) and 24 million cDNA reads (from 12 flowcells), all released on github. 

With both the RNA and DNA, even this set of highly experienced labs obtained greatly varying yields.

Still, getting hundreds of thousands of RNA reads is nothing to sneeze at (particularly since that would spread RNase around the lab!).

More importantly, a large number of the direct RNA reads -- and far more than the cDNA reads -- appear to represent full length transcripts.  Furthermore, the poly-A tail lengths can be accurately estimated with the direct RNA, even when they are hundreds of As long.

Basecalling accuracy is in the same neighborhood as DNA, with RNA performing slightly better.

There's a lot more in that README file -- identifying base modifications in RNA, capturing multiple splice forms, etc.  I'll try to dig more into that soon.

A number of users also presented exciting RNA results, particularly for direct sequencing of RNA viral pathogens such as flu and rabies.  I've put all the RNA-related tweets into a single Storify.

At least one talk debuted single-cell RNA sequencing on nanopore.  Another talk referenced Deb Peattie's pioneering work on chemical sequencing of RNA back in the 1970s.

Other User News

MinIONs continue to go to previously unimaginable locations -- perhaps the strangest one presented here was deep in a mine.  Nick Loman reviewed again his group (particularly featuring Josh Quick) sequencing Ebola and Zika in the field.  More tweets and talks in the a Storify focused on field uses.

Rachel Rubinstein of Ginkgo Bioworks described how a fast nanopore run saved hundreds of thousands of dollars by identifying the contaminating organism in a bioreactor. 

There were multiple talks on antibiotic resistance and pathogen detection (disclosure: my day job is looking for new antibiotics and I am doing light consulting for a company in the sequencing-by0-diagnostics space).   I've collected tweets on those topics in a Storify -- except a few I missed in preparing that from Claire Jenkins on getting pathogen sequence databases filled out.

Other worthy talks I'm going to reduce to tiny summaries: Steven Salzberg on assembling wheat,
Svetlana Madjunkova on pre-implantation genetic screening, Chia-Lin Wei on structural variants.  And so many more.  Watch my Twitter for announcements of a few more Storify pages from the 600 or so tweets which haven't been incorporated in the ones mentioned above.

On the Problem of Sequence Leakage

I've been spending some time lately in an unfamiliar world: the eukaryotic section of NCBI's NR protein database.  I've been almost exclusively a bacterial guy for six years, but the other side of starbase had an interest in find homologs of a particular protein so I went diving for some.  That experience has reminded me of two serious issues with public sequence databases.  Tonight I'll dash off a bit about one; expect the other complaint to show up in the not-so-distant future. And tonight's lament is the increasing dispersion of sequence respositories.

SmidgION: Mac Classic for the 21st Century?

Apple launched the Macintosh computer with a famous television ad playing on the launch year, 1984. What emerged was what we now know as the Mac Classic.  What may be less known is why the Mac Classic had that distinctive shape: it was intended to be backpack-portable, as Apple had a deal with a consortium of top U.S. universities to sell Macintoshes to their students.  Perhaps even more forgotten is that one of those schools, Drexel University in Philadelphia, made owning a Macintosh a requirement for students.

A Nucleotide Mixture-Based Error Correcting Short Read Chemistry

Sometimes polony-style short read sequencing seems like old news.  The underlying technology has been commercially available for over a decade.  I focus much of my attention to gains in long read technologies, though incremental improvements to read lengths or polony densities still appear.  Now in Nature Biotechnology a group from Peking University has published a new twist on sequencing-by-synthesis that is claimed to offer significant improvements on read accuracy.

AlphaGo & Biology

A comment was left on an early piece suggesting I comment on the recent AlphaGo paper and the possible applicability of this approach to biomedical sciences.  I'm not sure I have anything terribly original to say, but who can refuse a request?

Mission Bio Launches Tapestri Single Cell Platform

The fact that tumors and their immediate environment is genetically heterogeneous has long been known, but tools for high-throughput assessment of this heterogeneity have only recently become available.  The whole field of single cell RNA-Seq has seen spectacular growth, as new methods enable greater and greater numbers of cells to be profiled from a sample.  Profiling the DNA content on an individual cell basis has not been quite as much in the spotlight, but now a start-up called Mission Bio is launching a microfluidic library prep workflow, Tapestri, to enable amplicon panels to be run in single cell mode.

iGenomX Riptide Kits Promise a Sea of Data

A theme for me in my six years on Starbase has been addressing the challenge of cost-effectively sequencing many small genomes.  While sequence generation bulk prices have plummeted, all-in library construction cost has tended to stubbornly resist dramatic change.  Large genome projects don't face quite such a pinch, but if you want to sequence thousands of bacteria, viruses or molecular biology constructs, paying many-fold more for getting a sequence into the box than you're paying to move it through the box ends up being a roadblock. Illumina's Nextera approach dropped prices a bit, but not really a sea change.  Various published protocols drop  costs further via reagent dilution, but these can suffer from variable library yield and an increased dependence on precise input DNA quantitation and balancing.  Even then, the supplied barcoding reagents for Nextera handle at most 384 samples, and that is only a relatively recent expansion from 96. I previously profiled seqWell's plexWell kits, which like Nextera use a transposase scheme but with modifications to enhance tolerance to input sample concentration variation.  plexWell also enables very high numbers of libraries, which better mates projects with large numbers of small genomes to sequencers with enormous data generation capabilities.  Now comes another entrant in the mass Illumina library generation space: iGenomX, which has reformatted their chemistry from a microdroplet mode intended for linked read generation to a 96-well plate format requiring no unusual hardware.

PacBio's Frankenpatent on Error Correction

Well, here we go again.  Pacific Biosciences launched yet another patent lawsuit towards Oxford Nanopore at the end of September, and already the hounds are baying for me to look at the patents -- which I've foolishly established a reputation of doing. I will remind readers that, to use a construction that exasperates my son, I have no memory of these topics being covered during the time I was in law school. (said construction also works for divinity school, seminary, yeshiva, dental school, military academy, etc). 

Dispatches from CDC AMD Day 2017

I had the singular honor and pleasure of speaking this past Monday at the Center for Disease Control and Prevention's Advanced Molecular Detection(AMD) program's annual confab in Atlanta.  Just visiting the CDC campus was already a bit magical -- along with the Kennedy Space Center and Cold Spring Harbor it's one of mythical places of human exploration to me.  But to actually stand at the podium? Wow!

I've collected below a bunch of separate mental threads, many of which probably should be expanded out to a full post in the future.

Why Is LISP So Rare in Bioinformatics?

LISP is one of the oldest computer languages and perhaps one of the most influential of the early ones.  Some of the other well-known Eisenhower era languages -- Fortran, COBOL and ALGOL, have certainly left their mark, but LISP and derivatives such as Scheme or Common LISP certainly carries more cachet among "serious" programmers.  COBOL has always been a bit of an easy joke and Fortran tends to mark you as old-school; use of APL (once a language of mine) would mark you as dangerously reactionary.  ALGOL begat Pascal and Modula II and clearly had impact on the C syntax family of languages (including bioinformatics mainstays Python, Perl and Java) As I'll detail below, learning LISP has embarrassingly ended up stuck seemingly permanently on my future plans queue.  But that's also because life never forced the issue:  while LISP has certainly been used in bioinformatics (as covered in a review from 2016 ) , its mindshare in the community would seem to be very minimal.

Teaching Biology Evidence: Old or New?

I've been toying over a week with writing something based on an interesting Twitter discussion started by Dr. Laura Williams (@MicroWavesSci) of Providence College pondering the best way to approach teaching molecular genetics (really, science in general) at the undergraduate level.  In particular, Professor Williams wondered about the dangers of branding various key experiments with the names of the experimenters, such as Hershey-Chase or Meselson-Stahl.  The risk she points out is that this can devolve into an exercise in memorizing names and dates without assimilating concepts, or conversely that some students will find the names more of a hindrance than a help.  I'm going to play a bit with this, but I do emphasize that for her this is reality and for me it is a hobby (or perhaps a retirement fantasy, if I should ever actually retire).  Or in other words, for the academic this is her industry but for this industrial scientist it is academic.

The Curse of Spammotation Lives!

High throughput sequencing of genomes is over twenty years old, which demanded the development of automated pipelines for annotating this data.  I've worked on such pipelines since the early 1990s, implementing them as a student and at two different corporate stops.  Indeed, we were reviewing results from my pipeline versus some of the other ones out there to see what can be done better.  And unfortunately, I've found infuriating problems with RefSeq entries annotated with NCBI's bacterial genome annotation pipeline.  Now I'm usually one to sing the praises of NCBI -- they are a key resource for biological research and they make available multiple spectacular public services freely to the entire world.  But I'm afraid this time I need to vent.

DNA vs. the Machine

Last week's news contained a story sure to raise eyebrows.  A group of computer security researchers from the University of Washington claimed to have demonstrated that they could hijack a computer via sequencing a carefully-constructed DNA fragment.  Visions of NextSeqs rampaging through the streets immediately sprung to mind.  The paper is interesting and has some useful warnings for the bioinformatics community, but certainly the news coverage has been strong on hype and alarmism.

Computational Biology & Math: Am I Just Faking It?

Over on Quora a common type of question is "Can I be a computational biologist if I am now an X".  Personally I take a very broad view and think just about anyone with intellectual curiosity can become any kind of scientist.  A related type of question is "how skilled do I need to be in Y to succeed in computational biology", where Y is most often programming, biology or math.  I got thinking about this and started wondering whether I am actually at all skilled in math.  Here is the results of that analysis.

A Third GridION X5 Pricing Plan

When Oxford Nanopore announced their GridION X5 instrument in March, I and others attempted to parse the difference between the two pricing plans  -- and I made a bit of a hash of it.  The X5 runs 5 MinION flowcells independently in parallel from a single desktop instrument, which also includes FPGA-based acceleration of basecalling plus a license to perform sequencing-for-hire.  Indeed, Matt Loose tweeted out an image of an "X6" and then mention of an "X7"; the X6 had a MinION plugged into the USB port and apparently the FPGA unit can keep up with seven flowcells all running simultaneously.  Now Oxford has launched an interesting third "Starter Pack" plan that offers an even lower price point for the system.

STAT Proves Not Resistant To Antibiotic Tropes

Tuesday's Boston Globe carried a piece originating from STAT news on an interesting natural product antibiotic, pleuromutilin.  A research group recently published a new total synthesis of this fungal terpene, an advance which promises to enable greater medicinal chemistry around the molecule.  That part is cool.  Unfortunately, when it gets to the biology of pleuromutilin the piece by Eric Boodman completely spits the bit, trotting out some horribly inaccurate tropes.

New Life in the Sanger Market

In my bit on "I'm not dead yet" technologies recently, I included large scale Sanger sequencing. That reflects to a large degree my personal experiences and biases.  Targeted Sanger is great for spot checking the occasional junction or misbehaving clone or strain, but I forget that many clinicians still see it as a gold standard.  Apparently there are others who disagree with me, as Thermo Fisher recently launched a new Sanger instrument targeted at small labs, and according to GenomeWeb Promega plans an instrument offering in the same space as well.

Ice Ghosts:A Shortage of Maps

I'm going to step outside the usual topic space here and cover an interesting but frustrating book I read partly on the flight to London Calling (which is about the only connection it has to genomics).  Ice Ghosts, by Paul Watson, covers the searches for the lost Franklin Expedition, a mid-1800s British Navy attempt to find the Northwest Passage.  It's a pretty good book, after all it did win a Pulitzer Prize,  The topic is thrilling: explorers under difficult conditions and a mystery that lasted over a century.  There are lessons for science in general, such as the value in carefully evaluating oral histories that some would discard as unreliable. But what is maddening for me is that in a book for which a central theme is poorly understood geographies and their interpretations, the set of supplied maps fail miserably at assisting in the telling of the story.