Article recap: method biases in microbial community profilling of drinking water with 16S rRNA gene amplicon sequencing

In recent years, 16S rRNA gene amplicon sequencing has been widely adopted for analyzing microbial communities in drinking water. This has naturally lead to numerous publications relating to the drinking water microbiome. However, microbial analysis based on 16S rRNA gene sequencing is associated with inherent biases, and despite the popularity of the method within the field […]

>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 […]

ampvis2: A guide to ordination and how to use amp_ordinate in R

(This post is part of a series of ongoing posts about selected ampvis2 features) A common way for microbial ecologists to compare the microbial communities of different samples is by using ordination methods. These methods seek to highlight differences between samples based on their microbial community composition. By plotting samples as points in an x/y-plane, […]

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 […]

What is a good genome assembly?

With short reads you will often get fragmented but high single base accuracy assemblies  and with long error prone reads you can get a single contig assembly with just a few ultra long reads but with a lot of errors due to the lower read quality. Some of these errors can be fixed by adding more coverage […]