What a difference a day makes: markets react to PacBio's new sequencing platform

Daily change in share price at close of trade on October 1st, 2015:

Figures from Google Finance

Update: Earlier version of this figure incorrectly cited a 19% drop in Illumina's share price. My bad: -18.6 was the price change in dollars, not the percentage change.

 

Financial disclaimer: I do not own shares in any biotechnology company. 

How to sequence and assemble a large eukaryote genome with long reads in 2015 [Link] →

If you have any interest in the latest methods of DNA sequencing and/or genome assembly, you really owe it to yourself to be following Lex Nederbragt's excellent In between lines of code blog. Today's post offers some useful advice:

Main advice: bite the bullet and get the budget to get 100x coverage in long PacBio reads. 50-60x is really the minimum.

Who is saying what about the new PacBio Sequel system?

The big news from the world of DNA sequencing this week was that Pacific Biosciences has launched a new sequencing platform. The successor to their RS II platform has been named The Sequel System and it will be on display at the upcoming American Society of Human Genetics meeting. The new system promises a cost of sequencing a human genome (at 10x coverage) for $3,000.

The early buzz already seems pretty positive, and hopefully this sequel will turn out to be more like The Empire Strike Back than, say, Highlander II. What follows is a fairly comprehensive roundup of what people have been saying about this new platform — note that this story has been updated several times since I first wrote it (details of these updates are included at the end of this post):

From PacBio

From science news websites

'Traditional' news outlets

From blogs

From discussion forums

From the world of finance

I guess the question that everyone is asking now concerns the possibility of someone making a genome assembly from sequence data using this platform, and then using this tool to produce a better version of the assembly. In this case, would it be a sequel Sequel SEQuel genome assembly?

 

Questions from the conference call

There were a lot of questions asked in the hour long conference call. I've transcribed some of them and indicated the time point where you can jump to if you are interested in hearing PacBio's answers to specific questions:

  • 7:40:"Can you give us some thoughts on turnaround time and cost per genome?"
  • 11:20:"Can you talk about the use case beyond your current customer base? How this expands the number of applications?"
  • 15:17:"Can you help us think about some of the major changes that went into the system? Is there still a manifold that moves in three dimensions?"
  • 19:20:"From a user standpoint, are there any changes to site preparations that you would have to make from Sequel vs RS II; any limitations on things like putting it on 2nd/3rd/4th floor?"
  • 22:25:"You've introduced a number of kits with various applications for the RS II, will the Sequel be able to run all of the applications from the beginning, or will it take time to introduce certain applications to the system?"
  • 24:34:"Are there specific customer types that you think are positioned to be more on the earlier side of adoption, such as human sequencing, or microbiology, plant, animal etc.?"
  • 33:20:"Can you give a perspective on what the scalability of this platform looks like comparatively (to the RS II)?"
  • 35:08:"In terms of the metrics you gave around price per human genome, can you help us think about that relative to Illumina? If you take a 30x coverage genome on Illumina, what is the equivalent coverage you would need on the Sequel to get something similar…and how long would that take you to do?"
  • 38:29:"Recognising a lot has been achieved with this launch: different computer architecture, different form factor, new optical systems, higher density, with a smaller footprint. I just want to make sure, there's no compromise in raw accuracy expected relative to the RS II?"
  • 47:46:"Could you describe in layman's terms the benefits of methylation detection for your system?"
  • 50:50:"With your technology relative to other platforms, can you help us understand — if you have these larger pieces of the puzzle if you will — how advantageous that could be after you're done generating data, when you get down to assembling the genome?"
  • 53:16:"I'm curious what percentage of potential customers that looked at the RS II passed given the high price tag? What is the incremental buyer opportunity at the price point of $350,000?"
  • 57:35:"Still trying to understand what percentage of competitive platforms you think you can swap out with the Sequel?"
 

Updates

2015-10-01 13.46: Added some more sources of news, including questions asked in conference call
2015-10-01 20.04: Added in more conference call details, with time points of different questions.
2015-10-01 20.39: Added Keith Robison's blog post
2015-10-02 06:34: Changed link for Bio-IT World's piece
2015-10-02 09.08: Added more links about PacBio's presentation at ASHG 2015
2015-10-02 09.41: Added link to CoreGenomics post and added disclaimer
2015-10-02 11.54: Added links to Sequel-related discussions on SEQanswers and reddit
2015-10-02 13.28: Added Biomusings and Checkmate Scientist blog posts, and split main part of article into different sections
2015-10-12 09.52: Addition of NBC Bay Area News piece
2015-10-14 16.57: Addition of 2nd GenomeWeb story
2015-10-23 20.02: Addition of 3rd GenomeWeb story

 

Financial disclaimer: I do not own shares in any biotechnology company.

Question: when is a GitHub repository not a GitHub repository?

Answer: when it doesn't contain any useful code.

Update 2015-10-02 08.58: this post was updated to reflect the addition of code the metaPORE repository.

A discussion on twitter today revealed something which I find very disappointing:

A new paper by Greninger et al. (Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis) has been published in the journal Genome Medicine. The Methods contains the following line:

We developed a custom bioinformatics pipeline for real-time pathogen identification and visualization from nanopore sequencing data (MetaPORE) (Fig. 1b), available under license from UCSF at [23].

Reference #23 takes you to the metaPORE GitHub repository. At the time I initially wrote this post — and as the screen grab below shows — it contained zero code. Thankfully this has been changed and a set of Python and shell scripts are now available.

Maybe this was just some sort of error in scheduling the release of the paper and the code. However, journals and authors should understand that if a paper (or a pre-print) appears online and points to a code repository (or any other website), the expectation is that people should be able to visit the site in question and download code.