There is no doubt that long read DNA sequencing is transforming genome assembly for genomes at all scales due to the ability to span repetitive elements such as the rRNA genes. For years DNA sequencing has been the choice of either low accuracy (85-95%) long reads with systematic errors (pacbio, nanopore) or high accuracy (>99.9%) […]
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EliteForsk scholarship – failure is a virtue
[An expert is a person who has found out by his own painful experience all the mistakes that one can make in a very narrow field.] Niels Bohr, LIFE 1952 This quote by the famous Danish physicist Niels Bohr (1885-1962) nicely summarizes what science is all about – generating hypotheses and putting them to the […]
Why is it important to remove short molecules?
In the age of short read sequencing you could treat the cells with very harsh physical disruption as there was little chance that your DNA extraction could shear your DNA to shorter fragments than the machines could sequence. However, with the emerging long read sequencers short fragments are suddenly no fun and people have started […]
All I want for Christmas is a terabase of Nanopore data
Since November we have run 11 PromethION flow cells, generating >900 Gbp of data. It has been a journey of highs and lows, so we want to share what we have learned along the way. Our first lesson: it is important to use those flow cells ASAP! Despite our lab’s earlier success with a three […]
>100 Gbp on 1 flowcell outside ONT
After unboxing the Nanopore alpha-beta PromethION device some weeks ago and having our IT support/linux ninja help us integrate yet another box into the university network, we finally got around to run some PromethION sequencing again. We updated the PromethION software to Minknow 2 inserted a flowcell and it passed QC with 7000+ pores available […]
The Roblon Prize: my first prize
Each year, the Roblon foundation awards the Roblon Prize of 100,000 DKK (~16,500 USD), to a master thesis from Aalborg University acclaimed to fulfill the following: “The thesis should be of highest quality and innovative. It should have a positive effect on the research field as well as the future research and career of the […]
NCM17 – Day 2: Into the unknown
Day 2 at the NCM17 started, again, with Oxford Nanopore CEO Gordon Sanghera taking the stage, once again stating his dream that sequencing should be available to anybody, anytime, anywhere. There are currently around 12,500 mainframe DNA sequencers around the globe, a number he believes will be passed by ONT in a not too distant future. […]
NCM17 – Day 1: New tech and exciting applications
All the gear We start out with blazing punk rock (things are never too boring at Oxford Nanopore meetings) and plenty of promises from Oxford Nanopore CEO Gordon Sanghera. He gave us updates on various products, such as PromethION flow cells, which have been harder to produce than expected. However, we and others have now sequenced […]
Nanopore Community Meeting 2017: Prologue
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 […]
Populating the tree-of-life
Hi everybody and welcome to my first blog post at Albertsen Lab. As a newly started PhD student, I have engaged myself with the simple, yet Herculean task of populating the tree-of-life. As most people are aware of, microorganisms are more or less inescapably present in all places of the world — no matter how […]