Read Until

This documentation accompanies the preprint currently available BioRxiv.

The associated GitHub repository is here.

Read Until is a technology enabled by the Oxford Nanopore Technologies MinION and expected to be available in the future PromethION sequencers. The scripts described here provide one method of implementation of read until. The scripts are supplied as is and are used at your own risk.

MinKNOW 0.51.3 - 20th June 2016

The recent release of a new version of MinKNOW (cross platform) introduces a number of changes in the way Read Until is implemented, but importantly does now work. We are still testing this platform and will need to provide fresh instructions for configuring our scripts and test routines to work with this version. Some key changes are noted throughout these instructions - we welcome correspondence to resolve these issues!

We advise at this time waiting for the upcoming release of minKNOW (0.51.3.X) which will have increased stability for running read until. We know of one specific crash type which will result in the loss of control of sequencing. This is resolved in the upcoming release. We will update these pages as soon as this version is in the wild.

WARNING:

The read until API changes depending on the version of minKNOW in use. The read until API for minKNOW versions 0.48.1.3 - 0.51.1.51 is available on request from Oxford Nanopore.

Our code is compatible with all versions of the API. However, versions of minKNOW since 0.51.1.51 and up to 4th April 2016 do not function as anticipated. The ws_event_sampler simulations will work, but minKNOW itself does not function correctly with the API. This is actively being resolved by ONT. Thus, testing and simulation is possible with our code and later versions of minKNOW and ws_event_sampler but these scripts WILL NOT ACTIVELY REJECT READS AT THIS TIME with minKNOW versions >= 0.51.1.51. This is actively under investigation by ONT and updates will be posted here when this is resolved.

You must have minKNOW installed on the windows machine you are running this code on. ONT install Anaconda, a version of python, alongside minKNOW and this comes with some of the required packages for our scripts. Our scripts will also run on Linux or OSX but at this time we provide no explicit documentation to support this, however users confident with python and Unix should have no problems.

Risks!!

Running read until will influence the behaviour of your flow cell and change the output of your sequencing experiment. You are strongly advised to run simulations of read until prior to running on a live flow cell. The code as presented here is a demonstration of read until and one method by which it can be implemented. Users run this code entirely at their own risk.

Please note these scripts depend upon APIs which are not provided here. The Read Until API is available from Oxford Nanopore on request to MAP participants.

Getting help with read until.

We are happy to help where we can. Please feel free to contact via twitter @mattloose or email matt.loose@nottingham.ac.uk. We will try to update this read me file whenever significant changes are made to the API or minKNOW versions that might affect read until. For issues with the API itself or the ws_event_sampler program, users will most likely be redirected to ONT.