Rasmus Kirkegaard

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!

Wandering while wondering if this sample cup will hold a story exciting enough for @isme-microbes.bsky.social conference in New Zealand next year 🦠

I tested myloasm on a 50x Klebsiella isolate, and it was very fast - only took about 1 minute to complete (on my Macbook).

Will you be posting a comparison of wall time, CPU time and remaining errors for flye, autocycler, myloasm and metaMDBG? Think that would be really interesting 😁

Promising toolkit for binning and visualizing assembly graphs. The assembly graph is an underutilized source of binning information IMO
gbintk.readthedocs.io/en/latest/

It seems we can assemble (reasonably simple populations) of co-existing strains with ONT data now.

We assembled 6 single-contig Prevotella copri genomes of > 97% ANI for one metagenome. 4 of them were circular.

(The largest metaFlye P. copri contig was 13.4% complete)

Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social).

myloasm-docs.github.io

Most of the remaining errors are homopolymer-length errors, e.g. the genome had G×11 but the assembly had G×10. The rest are mostly 1-bp substitutions and indels. Often these occur at similar motifs within a genome.

Great update 🎉. Any idea of whether the few remaining errors are similar patterns?

New blog post!
In it, I benchmark the new version of Dorado from @nanoporetech.com, which comes with new DNA basecalling models. Short version: big accuracy gains for hac, small improvements for sup.
Check it out for the full results:
rrwick.github.io/2025/05/27/d...

Short-read metagenomic sequencing cannot recover genomes from many abundant marine prokaryotes due to high strain heterogeneity and platform-inherent GC bias (likely viruses, too), but Nanopore long reads can address this. A results thread on our recent preprint 🧵.

In addition to anti-GC and strain bias, certain taxa show systematically underestimated completeness via CheckM1 and 2, so historically much more likely to get erroneously thrown away in fragmented Illumina MAGs—a third reason for the existence of Ghost Taxa. A sub-sub-thread 🧵.

ARTIC 2 is here!

The planktonic microbiome of the Great Barrier Reef Large genome databases have markedly improved our understanding of marine microorganisms. Although these resources have focused on prokaryotes, genomes from many dominant marine lineages, such as Pela...

Very excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂

www.biorxiv.org/content/10.1...