We aR(10.)3 pretty close now!!!
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%) […]
AR(10)E we there yet?
Genome assembly has been a big challenge since the first methods for analysing DNA sequences saw the light of day. The challenge is primarily a result of our inability to read long fragments of DNA. With an explosion in the market for long read sequencing technologies (pacbio, nanopore, 10X, longas, etc) there is now hope […]
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 […]
What is wrong with correlating relative abundance? Everything!
(This post is the first in a small series compiled during my visit to Segata Lab in Trento, Italy) A provocative title I know, but as a young scientist venturing into the field of microbiology my concern about this is increasing to the point of now writing this blogpost. Sequencing data are inherently relative [Lovén et […]
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: The bread and butter of our amplicon analyses: amp_heatmap!
(This post is part of a series of ongoing posts about selected ampvis2 features) Now that the ampvis2 R package has got its own paper on bioRxiv it is a good time to also write a small blog post about our beloved heatmap, which Albertsen lab and the Center for Microbial Communities use in practically every […]