Adventures with the MinION II: Challenges and Drawbacks to the Novel Technology

Oxford Nanopore Technology’s (ONT) MinION has garnered considerable excitement, for good reason.  It’s suitable for labs on a limited budget, who work with DNA samples in the field, and who need long reads. These are all benefits that you cannot find when using other state-of-the-art sequencing technology (Visit ONT’s website here, to learn more about their mission). That being said, there is a substantial learning curve and considerable drawbacks to this novel machinery.

Functionality + Learning Curve:

First, achieving usable functionality comes with a difficult learning curve.  Mature NGS technologies are complex but  acquainting yourself with every step of the process is unnecessary because they have been appropriately optimized.  This is not the case with the MinION. The technology is still immature and rapidly developing. As a result, there is considerable optimization that needs to happen on the user’s end, requiring awareness of the device’s inner workings. Unfortunately, the company fails to provide easy access to basic information. Moreover, the majority of the introductory information is buried deep within the threads of the NanoPore Community.  Not only does this make finding information time consuming, but also frustrating.  Especially when you don’t know what to look for.  Easy access to pertinent information could decrease the learning curve for users and ease the burden of optimization.

Benefit of the Nanopore Community:

Luckily, the Nanopore Community has a plethora of useful information from expert users.  We have relied on this knowledge base many times to fix our own problems.  It is necessary to use the search function within the community to research information of interest.  Finding it difficult to use, we spent hours searching a phrase or keyword that left us with hundreds of threads. Furthermore, there is also considerable redundancy in many of the threads due to the lack of inaccessible information. If you are interested in educational material on the MinION, check out our first blog post in this series, here.

Possible Improvements:

The website does contain a ‘Knowledge’ page, that contains a myriad of technical documents (found here) that contain in-depth information. Unfortunately, these documents are not well advertised and require some digging around on their noisy website. Ideally, I would like to see a ‘Beginner’s guide to ONT’s technology’ which would include an overview of the Nanopore site, flow cell functionality, data acquisition, and recommendations for data analysis. With this technology you are making two costly investments, financial and temporal.  Reducing the learning curve (temporal investment) would make the technology more inviting and feasible for potential customers.

Difficulties with Optimization:

ONT is actively making attempts to optimize their novel technology.  By releasing improved versions of the device, changing the redox chemistry of the bulk solution, unveiling new prep kits, and discontinuing old ones, ONT is continually improving their devices.  Their improvement efforts are appreciated, but it has hindered our ability to emulate published protocols. Moreover, ONT has taken the backseat approach to trouble shooting by relying too heavily on the Nanopore Community to educate new users, identify existing problems, and develop data analysis tools. Check out their Getting Started FAQ page, here.  Notice, they fail to discuss any links or educational information pertaining to the specifics of the device.

Base Calling Software:

Figure 2: View of MinKNOW’s interface. The software assigns functional designations to each channels indicating their activity at the set voltage.

MinKNOW, the complimentary software from ONT, is responsible for a number of tasks.  Notably, it is responsible for data acquisition, real-time analysis and feedback, base calling, data streaming, device control, and sample identification.  Learn more about MinKNOW and data analysis, here and here. The interface is aesthetically pleasing and easy to use, but experiencing multiple software crashes has tainted my view of the tool.  Sadly, these crashes erase the statistics PDFs that contain useful information about the quality of the sequencing run and stop the run in its tracks.

Surprisingly, once assigned a technician to fix a large technological problem that we faced, they were exceptional.  While attempting to fix our software problem, the technician shared his intimate knowledge of the processes required to produce quality sequencing runs.  The technician was quick to offer any personal insight into our optimization problems and provide detailed explanations when asked specific questions.

If your lab is having trouble optimizing the MinION, check out the 3rd blog post, were we go over all the optimization techniques we have used.