Oxford Nanopore Updates: Reveals the nanopore used in Nanopore devices

Storified tweets from Oxford Nanopore’s technology focus Google hangout by Clive Brown.  Briefly,

  • Oxford Nanopore revealed the pore it uses in its devices. It is not MSP pore. :) It is using CsgG pore from E.coli. And it is using heavily engineered CsgG with over 700 mutations (with license) to make it a better pore for sequencing. Immediately after the update meeting, VIB/Vrije Universiteit Brussels announced that VIB’s Han Remaut has teamed up with Oxford Nanopore Technologies for the development of nanopore sensing technology.  Han Remaut group has been working on work on the protein nanopore, CsgG and will be in ‘R9’ in the MinION handheld DNA sequencer and the PromethIONTM system.
  • Oxford nanopore is seeing a big improvement in accuracy with R9 and new base caller. 85% accuracy in 1D and 95% accuracy in 2D. And Oxford nanopore is moving away from the current HMM-based base caller to Neural Network based base caller.
  • Oxford Nanopore's accuracy improvement with RNN and R9
  • March-April is pretty hectic for Nanopore, with lots of releases from Oxford Nanopore including the release of source code for base calling, Developmental R9, and first shipping of Promethion device.

Watch the Google hangout recording at You Tube.


  1. Michael D'Angelo says:

    Thanks for the post. I have a couple of comments to offer:

    1. Sounds like R9 is confirmed as being CsgG based, but there was no clarification of what R7 or earlier pores were based on. So it is still possible ONT were using MspA at some stage. I don’t know how this would affect the patent dispute, if there was a temporary infringement then a change to something new.

    2. I am struggling to understand how their CsgG pore can have 700 mutations. Based on the PDB entry you linked to above, the protein is only 277 amino acids long. Even if they meant nucleotide changes I’d be surprised if 700 could be made. Perhaps they mean they have analyzed 700 mutants to arrive at R9?

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