Highlights of Clive G Brown's Technical Update
Thu 29th September 2016
Clive G Brown, CTO of Oxford Nanopore, gave a technical update on 29th September.
Highlights from the talk include:
- A review of the nanopore technology platform, which is designed to enable the analysis of anything, by any person, in any environment.
- The same core technology is used in PromethION and MinION: real time, long reads, direct analysis, easy workflows
- The longest fragment sequenced at Oxford Nanopore so far is 510kb (255kb 2D), but you can choose the read length to suit you
- The technology has been iterated very rapidly but it is cross compatible (apart from the upgrade from the R7 nanopore to R9)
- Recent and imminent innovations include:
- Nanopore reader: R9 to R9.4. 1200 R9 mutants have been screened; this is faster and more accurate
- Enzyme motor: E7 to E8. DNA can be passed through the nanopore more rapidly, going from 250 bases per second per nanopore (bps) to 450 without losing accuracy
- Adapter components: upgrades reduce unnecessary pausing at the beginning of strands, enhancing yield
- Combining these updates, MinION Flow Cells now consistently yield >5Gb in the first 24 hours. Here is an example of a 9Gb run in 48 hours. See information below for October releases that will roll this performance out to customers.
- Moving from a Hidden Markov Model for basecalling to Recurrent Neural Nets has resulted in large accuracy improvements
- New SpotOn flow cells are now available. Easier to use and with a longer shelf life, they are now dispatched within 48 hours to US and EU, if you want them that fast. If not you can now schedule a specific dispatch date.
The following MinION releases will be available in October:
- New kits will enable 5-10Gb from a MinION Flow Cell
- Upgraded rapid 1D kit reduces library prep to 5 minutes and requires no additional reagents
- A new upgraded wash kit will be released, for using samples in series on the MinION. As a reminder, kits for barcoding 12 or 96 samples are already available
- Sequencing costs including the MinION, flow cells and kits will be ~$60/Gb (at 450bps) or $120/Gb (at 240bps)
- MinKNOW continuous improvements. There are now 3 ways to basecall in real time. Live & local, local & offline, in the cloud.
- An update on PromethION – the high-throughput, high-sample number desktop device. PromethION is designed to offer up to 144,000 nanopore sensing channels presented as 48 flow cells of 3,000 channels. (as a reminder, the MinION offers up to 512 channels) Because it is modular and streams real time data, it provides on-demand sequencing
- The PromethION Early Access programme (PEAP) is now open. Devices have been installed in the US and EU and flow cells are being shipped imminently. More information on how to join the PEAP.
- Specifications for both MinION and PromethION can be found here
What else is coming?
- Direct RNA sequencing kits will be released to early users in the next few weeks. If you are interested in trying direct RNA sequencing on the MinION, let us know.
- Registration for the VolTRAX Introduction Programme will open on 11th October and first devices will be shipped around the time of the Nanopore Community Meeting in early December. VolTRAX is a USB device for automated, reproducible, programmable library preparation.
- So that we can open up the use of nanopore analysis by any person and in any environment, we are developing a low cost consumable device for combined sample and library preparation. Project Zumbador is progressing well.
- Various methods of enrichment – analysing the DNA of interest where there is high background DNA – are already in use by the community. This might, for example, be used in infectious disease. We are working on a new proprietary method of directed pulldown to support rapid enrichment.
- Development of the SmidgION mobile-phone compatible DNA sequencer is progressing well.