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gringer writes:

You may recall that I did a TEDxWellington talk about a month ago. My talk was about sequencing on the Oxford Nanopore MinION [nanoporetech.com]. The video of this talk has now been edited and is available on the TEDx Youtube Channel:

https://www.youtube.com/watch?v=yTgZVVHJMlw [youtube.com]

Although I haven't explicitly said it in the talk, this is a live demonstration of DNA sequencing, and possibly the first such demonstration outside ones done by Oxford Nanopore Technologies. I spend the first half of the talk stalling for time while the initial QC finished, and then a bit of time after data analysis (i.e. a BLAST search) discussing where we could be heading.

To give a bit of an idea of the challenges involved in doing this, all my equipment for sequencing (excluding laptop) was brought to the venue the day before (for the dress rehearsal) in a 30cm polystyrene cube.

On arrival at the venue, I stored the ONT reagents in a freezer in the nearby kitchenette, and prepared the flow cell about half an hour before my talk. In my lab I had prepared two tubes with pre-mixed reagents (one with library + water + running buffer; one with fuel mix), so I was able to use a fine-nozzle pasteur pipette to do the final mixing and loading onto the flow cell.

I had a slightly flakey USB connection on the MinION, so couldn't start the run off-stage (it was very sensitive to bumping). Despite starting the run during the video prior to my talk, I still had a bit less run time than the 5 minutes I had planned for, so had to tweak my presentation a bit to fit the end of the QC step into my talk.

The sequencing run was carried out using a laptop I had purchased for $900 NZD and set up a couple of weeks prior to the conference. Sequencing was done from battery power only, using the WiFi connection because the wired connection was being used for conference live streaming -- this might be the reason why called sequences took a little longer than a couple of minutes to download onto the laptop. The dress rehearsal the day before was the first time I'd carried out a sequencing run on that particular laptop, and made me aware that the screen resolution was less than the recommended minimum requirements from ONT.

Despite everything that happened, I don't think any of the audience were aware that I had any problems with my run (apart from needing to use my dress-rehearsal backup sequences), which aligns very nicely with the themes of trust and secrecy for this year's conference.

For those interested in looking at the actual reads from that run, I've put the "pass" reads into a dropbox folder:

https://www.dropbox.com/sh/o7fz7s918...l-yOJggXa?dl=0 [dropbox.com]

If you want a little low-hanging-fruit programming project to work on, then you can have a look at improving the recently published open source base callers:

• DeepNano [bitbucket.org] (Neural network basecaller): Deep Recurrent Neural Networks for Base Calling in MinION Nanopore Reads; Vladimír Boža et al., Comenius University
• Nanocall [github.com] (HMM basecaller): An Open Source Basecaller for Oxford Nanopore Sequencing Data; Matei David et al., Ontario Institute for Cancer Research and University of Toronto

I have answered most of the questions that were put in the previous submission, and will put those answers as comments in this post if the editors don't transfer what I've already emailed to them. Please feel free to ask me any further questions, and I will try my best to answer them in this post, bearing in mind that I live in New Zealand and may take a bit of time getting around to an answer.

Original Submission