Nanopore Community Meeting 2017: Prologue

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Oxford Nanopore is hosting their annual community meeting in New York City this week. I’ll be there, thanks to being in top 5 of their one more flowcell competition – thanks to all that voted!

Although not as “big” as the London Calling conference they host, the line-up of speakers is impressive and promises talks on everything from megabase reads and gigabase yields to the newest assembly algorithms, field applications and maybe even some product updates? I’m excited! And in this blog post, I will give an overview of what I expect to hear at the meeting.

The first plenary speaker is Nick Loman, who, until recently, had the boasting rights of the longest read on the MinION. The record is now with Kinghorn Genomics, but still sits below the megabase read.

Although megabase reads may not be practical or strictly necessary for most applications, the importance of read length is bound to be brought up by Loman, who will also speak about the future of sequencing – sequencing singularity, as he terms it. I am also looking forward to hearing Ryan Wick speak as he will undoubtedly tell about his work with Unicycler, which we recently described as our preferred hybrid genome assembler. Wick will give us an overview of what to improve in order to obtain perfect assemblies (In general you should check his awesome analysis and tools hosted on github, see e.g. his comparison on current basecalling algorithms for Oxford Nanopore data).

In general, the algorithm developers are very well representated with both Sergey Koren, developer of Canu, who will give an update on assembling the human genome with ultra-long reads and Steven Salzberg that will present an update on their hybrid assembly method for large genomes (MaSuRCA), which is bound to be interesting (you should also check out his blog).

The current record holder in data yield, Baptiste Mayjonade, has a talk on day 1. It will be interesting to hear updates on yields from both researchers and Oxford Nanopore, as a lot of us are still struggling to reach the 10 Gbp. Perhaps with the right methods we could all compete with Baptiste’s 15.7 Gbp on a MinION flowcell? We could also hope for some updates on PromethION flowcell yields, although these are still under heavy development (we have been running our own PromethION, and are now waiting for next flowcell shipment – a blog post should be in the works..).

The last speaker of day 1 is Aaron Pomerantz, who has been sequencing barcoded DNA in a rainforest in Ecuador. There is also Arwyn Edwards on day 2, who has been sequencing in extreme environments. As I am working with on-site DNA sequencing myself, I am very interested in hearing more about these projects. The general trend lately seems to be increased portability, which will undoubtedly spark a wide array of new exciting projects and give insights into the ecology of the Earth.

Another session in my interest is the “metagenomics, microbiomes and microbiology” session on day 2, where my PI, Mads Albertsen, is giving a talk on metagenomics in the long read era. I am currently moving into the metagenomics field and hope to gain some insight in this session.

With some Oxford Nanopore talks throughout the two days, I hope to get some updates on the new tech released. I’m particularly interested in the “flongle” (the small and dirt-cheap flowcell), which I have heard might be ready soon. Recently, we have seen tweets about the first version of the all-in-one Zumbador, new lyophilised reagents being tested and the first version of chemistry for the VolTRAX sample prep device.

I am sure I will be wiser by the end of next week. I will be giving some daily digests here, so stay tuned. If you are going to NCM17 yourself, please come talk to me by poster 18 on Thursday 10.50-11.15 AM and 3.25-3.50 PM, and I can give you an overview of how we recently sequenced activated sludge samples on-site at a wastewater treatment plant (and on the way home).

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Martin H. Andersen

PhD student at Aalborg University
PhD student in the Albertsen Lab. I work with on-site DNA sequencing and long-read metagenomics. Interested in technology, gastronomy and everything in-between
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  1. Pingback: NCM17 – Day 1: New tech and exciting applications – Albertsen Lab

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