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.