My first response when arriving at the meeting was that I took a wrong turn. The venue was very flashy, polished and professional. So much so, I felt like I ended up at an Apple launch event! But my nametag was there, and listening more closely it transpired I ended up in Little Britain. Not surprising, given Oxford Nanopore Technology (ONT) hails from overseas.
ONT, the company organising this meeting, is probably best known for their hand-held sequencer, the MinION. This fancy machine, about the size my first mobile, a – yellow – Nokia 5110, can be used in the lab as well as the field to generate long reads, thousands to over a hundred thousand bases in length. A great feat, but also something that still requires a lot of tweaking and troublesooting, which is why this community meeting was so beneficial for both ONT and its users.
When the talks started it quickly became clear there was more to the meeting than an amazing venue. Talks were of a wide diversity and good quality. We were introduced to technological improvements, including an even smaller sequencer (SmidgION), new reagent kits and molecular protocols as well as a wide range of topics where ONT sequencing played an important role. Diagnosing malaria in India, looking for complex genomic rearrangements in Caenorhabditis elegans and sequencing the human genome were but a few of the exciting topics.
Over the two-day meeting, I got most out of the breakout sessions where there was ample opportunity for discussion following a set of flash talks. These were talks of the people that were getting their hands dirty. Be that in the wet lab, in the field, or behind their computers.
Arwyn Edwards, from Aberystwyth University, gave the talk that stood out most to me. He started out introducing us to cryoconite, a dust partially made up of microbes. When this dust builds up on glaciers, its dark appearance accelerates melting. For studying which microbes are present, he uses the MinION. I have a warm, well-equipped lab at my disposal, but was intrigued by what must be the most high-tech lab-in-a-bag ever. Everything from sampling, DNA-extraction, sequencing and analysis fits in this army-style rucksack and allows Arwyn and his team to study the microbe composition on site (dubbed extreme metagenomics). Evidenced by twitter, I was not the only one enthralled by this travelling lab!
Having done a lot of optimizing myself, it was interesting to listen to the approaches others took to tackle the same issues, and, often, come to the same conclusions. This was valid for both the molecular work as well as the concerns we were having about the computational analysis. Especially with regards “what is good data?” when sequencing longer fragments. Consensus is: with long read technologies coverage gives way to longer reads when assembling new genomes. Aiming for fewer but longer reads rather than more “short” (few kb) reads is the way forward.
Finally, a blog on this conference wouldn’t be complete without a mention of the amazing care they took of our nutritional needs. From breakfast to dinner, everything was equally tasty and well prepared. For vegetarians and meat lovers alike, there was plenty for everyone. The eye for detail was amazing, and provided an excellent souvenir for avid tea-drinker James.
I look forward to further collaborations with those I connected with at the meeting, and would like to thank HPI and the Faculty of Veterinary Medicine at the University of Calgary for supporting my attendance.