Rasmus Kirkegaard

Postdoctoral position on methanotrophic bacteria - Vacancy at Aarhus University Vacancy at Department of Biology - Microbiology, Aarhus University

I'm recruiting a postdoc to figure out how aerobic methanotrophic bacteria oxidise methane in anoxic freshwater sediment environments: international.au.dk/about/profil... Come to Aarhus University in Denmark and work on this 2-year project funded by @villumfonden.bsky.social!

You load one @nanoporetech.com flowcell and it almost ruins your day 💩💩💩. You load six more and they look stunning 🟩💚🟩💚💚🟩

Still 10 days left to apply! 🦠🧪👩‍🎓🔬
Come work with my team in beautiful Vienna!

I miss our P24 for doing runs like that. P2s are fine but there is something satisfying about the many spots...

208Gb and can't tell you because it was for a customer
@timdepooter.bsky.social

High yields are nice, but I think more important is highlighting the current robustness of the PromethION platform. In 2 weeks we processed 48 FC's resulting in 7.4Tb of data. That's over 150GB per FC on average. We definitely need to start thinking about mutliplexing. @nanoporetech.com

Professor or Associate professor (Tenure Track/Full) in Microbial Genetics of Health - Turun yliopisto - Työpaikat - Duunitori Avoin työpaikka: Professor or Associate professor (Tenure Track/Full) in Microbial Genetics of Health - Turun yliopisto, Turku. Duunitorilla lisäksi yli 30 000 muuta avointa työpaikkaa. Lue lisää nyt!

Professor (full) or Associate Professor (tenure track) in Microbial Genetics of Health (U. Turku Finland). Competitive starting package included! Please share.

duunitori.fi/tyopaikat/ty...

193-200Gbp without any washing step (sewer biofilms & soil enrichments) ❇️🚀

Will there be a response time limit? Imagine I contact everyone would they need to reply in e.g. 2 weeks? Will there be an expiry date for data or can I expect to be contacted in 40 years for some old stuff?

Wow! I am very much against this. The deep value of GenBank is in it being a public domain database with 0 limitations on use.

The norm that when we publish, we share the sequencing data supporting its claims *with 0 limitations on use* is so important for open science. I hope it doesn't change!

How many authors would you need to contact to run mining on the entire SRA? I can imagine signing up to be contacted would put me in risk of a DDOS attack with all the automated requests?

What is your highest yield on a @nanoporetech.com flowcell? And what was the sample type?

Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats - Nature Microbiology Nanopore sequencing of Danish soils and sediments yields genomes from over 15,000 microbial species, expanding the phylogenetic diversity of prokaryotes by 8%.

Ahh, have you seen this one? To me, this is the crown jewel of long read metagenomics at the moment? Gives some guidelines on how deep you need to sequence soil to get decent MAG recovery.

www.nature.com/articles/s41...

Have not done much @nanoporetech.com sequencing lately but this looks pretty 🟩🟩🟩🟩🟩🟩 #MFDExtreme

Gotta catch em all! A little late night sampling for the MFD Extreme project. What microbes call this sand their home?

Beautiful evening for sampling. Microbes live in so many funky places and I finally got the chance to hunt them in locations that were not wastewater treatment plants 🎉🦠🧬🇩🇰 #MFDExtreme

Slowly it's sinking in 😍
Very excited about my new role as #Assistant #Professor @univie.ac.at @cemess.bsky.social! 🦠👩‍🎓🔬

It's great to be part of this fantastic team of friends and colleagues!

🧪 #Microsky

Quality scores seem to be pretty well calibrated but is a bit conservative which is probably better than being overly optimistic. Mappings with 100 % identity hits come from a wide range of quality scores

28 kbp

N50 was 11 kbp. Did not shear it. The longest perfect read stretch was 28kbp. When our servers behave again I will start uploading it.

We have a new 3-year postdoc position in our group at the @hifmb.de to study plasmids and plasmids systems of the marine environment to survey their utility in microbial responses to environmental change.

Please see the official job ad here, and spread the word:

jobs.awi.de/Vacancies/20...

Can we please get Dorado 1.0.0+ in @nanoporetech.com minknow ASAP? 4090 also jumps quite a bit and is getting closer to support a full P2S with live sup 🎉

Safety – Waymo At Waymo, we are as rigorous and innovative in our safety practices as we are with our technology. We’ve built a comprehensive safety program to guide our testing and development of fully autonomous d...

Where are you in the process of pushing for Waymo to enter Europe and reduce injury causing crashes by 80 %? waymo.com/safety/

Do you have a sketch of the design to make a better suggestion than OpenReadingFrameSensor. How many ORFS do you plan to sell?

GitHub - Kirk3gaard/2025-Crowdsource-GPU-basecalling-stats: A repository for collecting GPU basecalling stats A repository for collecting GPU basecalling stats. Contribute to Kirk3gaard/2025-Crowdsource-GPU-basecalling-stats development by creating an account on GitHub.

It is the zymo HMW subset that I use for the gpu stats (github.com/Kirk3gaard/2...) . Will give the full set a go at next week and release some info along with the reads.

~20 times more than sup.

What kind of sensors etc? What will it measure?

Even some pretty long reads in the 100 % identity pool.

Got a chance to take the @nanoporetech.com hyp(er accuracy) model for a spin. Pretty decent improvement in read quality 🚀 but expect to spend quite some more GPU hours 😉

(Reads were mapped with minimap2 and identity scores from nanoplot were used for phred score calculations)

With all that is happening it is very exciting to see the Price Lab's very first, in-house, Oxford Nanopore direct RNA seq running! Not bad for a ~3 year expired flow cell!