Lightnews — Scholar-powered news

Rasmus Kirkegaard

@kirk3gaard.bsky.social

450 followers 250 following 79 posts

Staff scientist having fun with DNA seq and bioinformatics at #AlbertsenLAB

Posts Media Videos Starter Packs

Pinned

Rasmus Kirkegaard @kirk3gaard.bsky.social · Mar 21

Want @nanoporetech.com data for benchmarking microbe related stuff? Check our data for pure cultures,
@zymoresearch.bsky.social mocks and metagenomes ( github.com/Kirk3gaard/M...). Basecalled reads with methylation is in @enasequence.bsky.social . Eventually the pod5s might go there as well.

GitHub - Kirk3gaard/MicroBench: Overview of our data for microbial genomic benchmarking

Overview of our data for microbial genomic benchmarking - Kirk3gaard/MicroBench

github.com

7 17

Reposted by Rasmus Kirkegaard

Ian Marshall @ianpgm.bsky.social · 5h

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!

Postdoctoral position on methanotrophic bacteria - Vacancy at Aarhus University

Vacancy at Department of Biology - Microbiology, Aarhus University

international.au.dk

12 7

Rasmus Kirkegaard @kirk3gaard.bsky.social · 1d

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

Reposted by Rasmus Kirkegaard

Kathi Kitzinger @kathikitzinger.bsky.social · 3d

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

Kathi Kitzinger @kathikitzinger.bsky.social · Aug 4

🚨3-yr Postdoc Position on #SingleCell Activities in #Marine #N-Cycling🦠🧪👩‍🎓🔬

Join me @univie.ac.at @dome-vienna.bsky.social
Part of our ERC Synergy #RECLESS looking at microbes in marine oxygen minimum zones

Apply by Oct 15, start March 2026!

-> ucloud.univie.ac.at/index.php/s/...

RECLESS_Postdoc_single_cell_UniVie.pdf

u:cloud - Ihre Daten, auf Wolken gebettet.

ucloud.univie.ac.at

2 2

Rasmus Kirkegaard @kirk3gaard.bsky.social · 7d

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

Reposted by Rasmus Kirkegaard

Wouter De Coster @wdecoster.bsky.social · 7d

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

1 1 3

Reposted by Rasmus Kirkegaard

Tim De Pooter @timdepooter.bsky.social · 7d

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

1 1 6

Reposted by Rasmus Kirkegaard

Teppo Hiltunen @teppo-h.bsky.social · 8d

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...

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!

duunitori.fi

50 34

Reposted by Rasmus Kirkegaard

joanaseneca.bsky.social @joanaseneca.bsky.social · 10d

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

1 1

Rasmus Kirkegaard @kirk3gaard.bsky.social · 11d

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?

Reposted by Rasmus Kirkegaard

Alex Crits-Christoph @acritschristoph.bsky.social · 11d

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!

3 3 10

Rasmus Kirkegaard @kirk3gaard.bsky.social · 11d

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?

1 4

Rasmus Kirkegaard @kirk3gaard.bsky.social · 11d

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

Reposted by Rasmus Kirkegaard

Steven Robbins @stevenjrobbins.bsky.social · Aug 14

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...

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%.

www.nature.com

1 1 2

Rasmus Kirkegaard @kirk3gaard.bsky.social · Jun 24

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

Rasmus Kirkegaard @kirk3gaard.bsky.social · Jun 24

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

Rasmus Kirkegaard @kirk3gaard.bsky.social · Jun 21

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

Reposted by Rasmus Kirkegaard

Kathi Kitzinger @kathikitzinger.bsky.social · Jun 19

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

Michael Wagner @michiwagner4.bsky.social · Jun 7

So happy to read these @cemess.bsky.social news. Our centre at @univie.ac.at is really well positioned for future developments

@kathikitzinger.bsky.social
#MichaelZumstein

🧪 #Microsky

1 27

Rasmus Kirkegaard @kirk3gaard.bsky.social · Jun 16

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

1 2

Rasmus Kirkegaard @kirk3gaard.bsky.social · Jun 13

28 kbp

1 1

Rasmus Kirkegaard @kirk3gaard.bsky.social · Jun 13

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.

Reposted by Rasmus Kirkegaard

A. Murat Eren (Meren) @merenbey.bsky.social · Jun 5

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...

PostDoc in ecology and evolution of plasmids in polar waters at HIFMB (f/d/m)

Layout AWI HIPP extern, englisch

jobs.awi.de

2 85 79

Rasmus Kirkegaard @kirk3gaard.bsky.social · Jun 6

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 🎉

Rasmus Kirkegaard @kirk3gaard.bsky.social · Jun 6

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

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...

waymo.com

Rasmus Kirkegaard @kirk3gaard.bsky.social · Jun 5

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

1 1

Rasmus Kirkegaard @kirk3gaard.bsky.social · Jun 5

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.

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.

github.com

1 1