Clive G Brown: CTO plenary from London Calling
Wed 30th May 2018
In May 2018, 600 people gathered at Old Billingsgate in London to share their experiences of nanopore sequencing. Clive G Brown, CTO of Oxford Nanopore, gave a plenary that described recent advances and the vision for nanopore technology.
The talk included:
An introduction to nanopore sensing. Fully scalable, nanopore sequencing offers long reads, direct analysis, real time data and scalability. Which device is right for you?
Or if you would rather use a service provider, you can find a supplier offering sequencing on GridION or PromethION here.
Introducing the forthcoming 'D Chip' - Oxford Nanopore has achieved 30Gb on a MinION Flow Cell with this upgrade. Conference attendees were given a free D Chip in their welcome bag.
A review of PromethION, which is now 'out of the gate' as Oxford Nanopore achieves up to 170Gb on one flow cell and users in the community are closing in on 100Gb. As a reminder, PromethION is designed to run up to 48 such flow cells, on-demand. Clive announced that the PromethION Early Access Programme is closed and the PromethION starter pack and top up flow cells are now commercially available in store.
Clive reviewed the latest release of MinKNOW 2.0. This software upgrade improves performance but also makes nanopore sequencing easier to run.
Clive noted that as Oxford Nanopore develops its products to be easier to use and accessible to more people, it's important to make sure that computing/data analysis are as easy as sequencing. We are now launching MinIT, a compute accessory for MinION or Flongle. More information about MinIT is available here.
Clive noted that we are planning to integrate the MinIT with MinION, to make the MinION Mk 1c - to integrate sequencing and computing.
Clive reviewed recent an imminent chemistry upgrades, in particular the improvements that have been delivered by R9.4.1 and RAD004, which gave greater yields, including when selecting very long reads. The community is also driving ultra-long reads, for which the record is now nearly 2.3Mb as a continuous read. Evolutions in basecalling were also reviewed, including a recent update on chunk size that is configured to better deal with repetitive data such as structural variation. To recall, 1D^2 kits combine template and complement data from two reads. Oxford Nanopore is now developing a 1D^2 amplicon kit.
Clive reviewed the strategies that Oxford Nanopore is using to remove the last few bugs in consensus accuracy, including approaches in basecalling, assembly tools and chemistry. For example, recent tools that are helpful include Medaka (open source, fast consensus correction, achieving similar results to nanopolish) and Miyagi, which improves on nanopolish results by adding in dwell time sequence context for homopolymers.
Clive reviewed Flongle, a flow cell ‘dongle’ that works with MinION or GridION. It enables smaller, individual, rapid and low cost DNA/RNA sequencing tests. Flongle production is gearing up for early access timing. Early access packs will be available, $90-104 per single-use.
Clive then returned to the mysterious live demo that had been taking place to the side of the stage - using a sample of his saliva. With a thumbs up, the demo of 'Project Zumbador' showed a new solution to sample extraction and preparation, with low cost, rugged materials and delivering a rapid result. Clive revealed the name of this product: Ubik.
Continuing on the theme of making preparation easier, Clive reviewed VolTRAX, the automated, programmable preparation device. With VolTRAX v1 now tested in the community, we are now bringing you VolTRAX v2. It has more features including heating/cooling/thermal cycling, precision controlled magnetic beads, and we will be releasing a wider range of protocols in the coming months. The VolTRAX Introduction Programme VIP will be retired in June, when VolTRAX v2 will be available at our online store.
Clive wrapped up with 'Skunkworx' projects, where he outlined the possibilities for using the VolTRAX platform for ambitious, complex and large scale projects - for example, sequencing on VolTRAX, and even single cell analyses.