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 […]
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 […]
Can you beat our Nanopore read error correction? We hope so!
Tagging of individual molecules has been used as an effective consensus error-correction strategy for Illumina data (Kivioja et al 2011, Burke et al 2016, Zhang et al 2016) and the principle is similar to the circular consensus sequencing strategy used to generate consensus reads with error rate of < 1 % on the PacBio (Travers et […]
Starting from scratch – building a package in R
For the first time, I am going to share something more related to my master thesis. When I started this thesis, I did not know how to use R. In order to learn R, I started using DataCamp, which is a series of interactive courses. You can start from scratch and build your skills step […]
Analysing amplicon data, how easy does it get?
Ever done amplicon DNA sequencing of the 16S rRNA gene to identify microbes? If so, then you must know about the challenge of analysing such complex data easily. My name is Kasper, and I am currently a master student here at the Albertsens lab. When I first learned how DNA is sequenced today, I was astonished by the rapid […]
Traversing the fog… Soon graduating – then what??
The other day I watched my boyfriend playing the game Dark Souls III. At some point he had to step through this fog, entering a new area or a boss area or something else. You never know. It was a boss, but I don’t remember how it went from that point on. Because it got […]