Rasmus Kirkegaard
@kirk3gaard.bsky.social
π€ 507
π₯ 263
π 142
Staff scientist having fun with DNA seq and bioinformatics at
#AlbertsenLAB
pinned post!
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.
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GitHub - Kirk3gaard/MicroBench: Overview of our data for microbial genomic benchmarking
Overview of our data for microbial genomic benchmarking - Kirk3gaard/MicroBench
https://github.com/Kirk3gaard/MicroBench
about 1 year ago
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Rasmus Kirkegaard
Ryan Wick
5 days ago
New blog post! I analyse the new
[email protected]
basecalling model from
@nanoporetech.com
and discuss the conspicuous lack of a new sup model:
rrwick.github.io/2026/06/11/d...
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Dorado v2.0.0: no more sup?
a blog for miscellaneous bioinformatics stuff
https://rrwick.github.io/2026/06/11/dorado-v2.html
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Is
@nanoporetech.com
hac v6 better than 5.2.0 sup? The short answer is no. But are a few errors in a genome worth 5 times more basecalling compute?
github.com/Kirk3gaard/M...
7 days ago
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Rasmus Kirkegaard
Oxford Nanopore
8 days ago
Without trusted references, methylation data is hard to interpret. Using ATCC Genome Portal resources and nanopore sequencing, this webinar shows how to turn raw microbial modification signals into biological insight.
https://bit.ly/4o369uU
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Steven Robbins
11 days ago
It's also a boon for service providers with proms and high throughput. Many users can't/don't rebasecall and running sup on-machine limited the # of flow cells that could be run. v6 hac model means that more flow cells can be run concurrently to provide Q23 data directly for clients to run with.
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Rasmus Kirkegaard
Jean P. Elbers
11 days ago
Hac 6.0.0 seems like a mixed bag to me compared to sup 5.2.0 based on
github.com/Kirk3gaard/M...
. Thanks for your hard work
@kirk3gaard.bsky.social
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https://github.com/Kirk3gaard/MicroBench/blob/main/analysis/zymohmw/README.md
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Steven Robbins
11 days ago
Thought i'd highlight that the ONT London Calling tech talk is now up. Points of interest for the microbiome community: 1) Direct RNA multiplexing now available. Can now run 24 samples per flow cell, recover full-length transcripts with 8 base pair modifications...
www.youtube.com/watch?v=CE69...
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London Calling 2026 Technology update
YouTube video by Oxford Nanopore Technologies
https://www.youtube.com/watch?v=CE69zsHfbGM
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Rasmus Kirkegaard
Heng Li
17 days ago
Jeremy Wang developed rammap, a minimap2 rewrite in Rust. It achieves comparable or better performance than minimap2 and produces identical output to minimap2. During rewrite, Jeremy found two long-existing bugs in minimap2 which are fixed in v2.31.
www.biorxiv.org/content/10.6...
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https://www.biorxiv.org/content/10.64898/2026.05.26.726289
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For many years you needed UMIs and similar dark molecular biology magic to get perfect amplicon sequences from
@nanoporetech.com
data. With recent accuracy improvements+really clever algorithms that is now changed. Savont unlocks ASVs from low coverage nanopore amplicon data π€―π€―π€―
add a skeleton here at some point
16 days ago
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Rasmus Kirkegaard
Human Pangenome Reference Consortium
20 days ago
Abstract submissions for the T2T Face-to-Face conference are open through June 15th!Β Join the community Sept. 3β4 in Santa Cruz, CA, for two days of discussion and collaboration around telomere-to-telomere genomics and pangenomics. Learn more:
sites.google.com/ucsc.edu/t2t...
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When you run out of slots on the P24 it is handy to have a bunch of P2 solos π©π©π§¬
@nanoporetech.com
25 days ago
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Rasmus Kirkegaard
Josh Quick
25 days ago
New preprint from us! π¦ Clinical metagenomics is great for sequencing pathogens directly from patient samples but for some protocols sensitivity for RNA viruses lags behind bacteria & fungi. We have shown why, and how to fix it.
www.medrxiv.org/content/10.6...
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Library preparation strategy critically impacts RNA virus sensitivity in clinical metagenomics
Clinical metagenomics uses sequencing for culture-independent identification of pathogens directly from clinical specimens. While a number of protocols claim to be pathogen agnostic, sensitivity for R...
https://www.medrxiv.org/content/10.64898/2026.05.18.26353500v1
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On this day in 2015 a disruptive company handed out DNA sequencers in goodie bags π€―π€―π€―. Next week
@nanoporetech.com
is hosting their yearly London Calling event. Bring back disruption π§¬π
about 1 month ago
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The nvidia dgx spark is a cool box but you get more
@nanoporetech.com
basecalling for your money with one of the other options (
github.com/Kirk3gaard/2...
)
about 1 month ago
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Ever wondered what microbes you could find in Denmark? Pupils from Danish schools collected soil samples across the country so you can now browse the microbes (
cmc-aau.github.io/masseeksperi...
).
about 1 month ago
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Rasmus Kirkegaard
bioRxivpreprint
about 2 months ago
Performance Test of the QNome Nanopore Sequencer
https://www.biorxiv.org/content/10.64898/2026.04.29.721586v1
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Similar situation in academia when the professors "win money" to the university π€£
add a skeleton here at some point
about 2 months ago
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Full
@nanoporetech.com
deck Friday ππ§¬ππ©π©π©
about 2 months ago
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Anyone happen to have a dgx spark doing nothing? Benchmark it for
@nanoporetech.com
basecalling (
github.com/Kirk3gaard/2...
)
about 2 months ago
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Why would
@nanoporetech.com
minknow produce fast5 files in 2026???
about 2 months ago
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More do it at home
@nanoporetech.com
sequencing is being announced on X (
x.com/SethSHowes/s...
) A blog post by Seth Howes (
iwantosequencemygenomeathome.com
). Hope London Calling will feature a tinkerer session this year.
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https://x.com/SethSHowes/status/2045782975380406623?s=20
about 2 months ago
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Steven Robbins
2 months ago
There's a reason why most undiscovered taxa come from soils, sediments, wetlands, etc:
www.nature.com/articles/s41...
The way I prefer to think about it is to put that money into long reads and get usable data.
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Unbinned contigs expand known diversity in the global microbiome - Nature Microbiology
Re-analysis of over 92,000 metagenomes reveals hundreds of thousands of previously undescribed Bacterial and Archaeal clades hidden in plain sight.
https://www.nature.com/articles/s41564-026-02314-6
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Rasmus Kirkegaard
Earth BioGenome Project π
2 months ago
A major milestone for biodiversity genomics: EBP-affiliated projects have now contributed over 6,000 genome assemblies toward the goal of sequencing all known eukaryotic life. 𧬠Thank you to all EBP-affiliated projects behind this work, from sampling and DNA extraction to sequencing and assembly.
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Rasmus Kirkegaard
Shuai Wang
3 months ago
Our ECE-host framework doesn't care which sequencing platform you useβitβs ready to go once you have mod calling results. The kicker is that we need scalable mod calling from metagenomics. If it doesn't scale, the ECE-host analysis can't happen.
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Rasmus Kirkegaard
The Banfield Lab
3 months ago
Congratulations
@wshuai.bsky.social
and co-authors! Weβre excited to introduce MODIFI, our new scalable method for detecting DNA modifications in PacBio metagenomic data and estimating ECE-host linkage. Check out the preprint:
www.biorxiv.org/content/10.6...
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https://www.biorxiv.org/content/10.64898/2026.03.27.714056v1
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Jean P. Elbers
3 months ago
videocardz.com/newz/hp-unve...
wow, 4 Nvidia RTX Pro 6000 Blackwell GPU support. Future Oxford Nanopore attachment for the P48 sequence?
@kirk3gaard.bsky.social
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HP unveils Z8 Fury G6i workstation with quad RTX PRO 6000 Blackwell GPUs offering 384GB VRAM - VideoCardz.com
HP Z8 Fury G6i supports up to four RTX PRO 6000 Blackwell GPUs HP has introduced the Z8 Fury G6i, a new high-end workstation built around Intelβs Xeon 600
https://videocardz.com/newz/hp-unveils-z8-fury-g6i-workstation-with-quad-rtx-pro-6000-blackwell-gpus-offering-384gb-vram
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Rasmus Kirkegaard
Jim Shaw
3 months ago
_720 Gbp_ marine nanopore metagenome -> 328 circular prokaryotic contigs: using myloasm! Insane work by Lui and Nielsen. Also shows how modern long read assemblies can disentangle coexisting strains and reveal ecological insights.
add a skeleton here at some point
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Keith Robison
3 months ago
ElysION Fields
omicsomics.blogspot.com/2026/03/elys...
π§¬π₯οΈ
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ElysION Fields
Even before new CEO Francis Van Parys took the reins at Oxford Nanopore with the start of the month, the company had made yet another primin...
https://omicsomics.blogspot.com/2026/03/elysion-fields.html?m=1
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Will 2026 be the year we finally see something new from
@nanoporetech.com
or are we stuck due to the clinical focus? Next generation ASIC chips would be the opportunity to align product lines. One flowcell to rule them all?
3 months ago
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Rasmus Kirkegaard
Morten Kam Dahl Dueholm
4 months ago
A new era for
#ONT
amplicon sequencing? We show that
#ONT
#amplicon
sequencing now achieves accuracy sufficient for
#ASV
resolution using standard Illumina-based pipelines. We validated this by sequencing identical amplicons on
#ONT
and
#PacBio
.
@nanoporetech.com
www.biorxiv.org/content/10.6...
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The sun brings out the green
@nanoporetech.com
π©π©π©π©π©π𧬠Happy Friday everyone.
4 months ago
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Rasmus Kirkegaard
Edward Nirenberg
4 months ago
It is absolutely outrageous that Modernaβs flu vaccine was met with a βrefusal-to-fileβ even after their approved their protocol with FDA and carried out the trial as agreed. This vaccine works better in older adults than the current flu vaccines.
apnews.com/article/mode...
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Moderna says FDA refuses its application for new mRNA flu vaccine
The U.S. Food and Drug Administration is refusing to consider Modernaβs application for a new flu vaccine made with mRNA technology.
https://apnews.com/article/moderna-vaccine-flu-mrna-2fc551cb2fb45735e67db0a4e2e2b0fb
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Hey
@bsky.app
can we get a poll option?
4 months ago
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Rasmus Kirkegaard
James Ferguson
4 months ago
claude: I have no idea why we now have more unmapped reads than before after adding in mismatch scoring me: did you reverse complement the genome sequence? claude: i'm a dumbass
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Rasmus Kirkegaard
Oxford Nanopore
4 months ago
New hifiasm-ONT assembly method delivers high-quality, cost-efficient near T2T assemblies using standard Oxford Nanopore Simplex reads, broadening access to comprehensive genome assemblies across research and clinical applications.
https://bit.ly/4awzU15
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Dan Portik
5 months ago
I think Single-M was written with that use-case in mind. Haven't tested it personally so can't vouch for it, but likely worth a try.
www.nature.com/articles/s41...
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Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper - Nature Biotechnology
Novel microbial species in metagenomes are identified using conserved regions within universal marker genes.
https://www.nature.com/articles/s41587-025-02738-1
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Rasmus Kirkegaard
Paul Orwin
5 months ago
interesting nanopore sequencing experience. found this in the middle of my genome assembly. driven by a single read with a big homopolymer in the middle of it? pretty weird, something to look out for i guess (i wonder how many of these are in Genbank...)
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With the P2S joining the long list of abandoned
@nanoporetech.com
products in favour of the expensive P2i it becomes clearer that the
#anyone
#anywhere
vision is lost...
5 months ago
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Rasmus Kirkegaard
Jeremy Wilkinson
5 months ago
Iβm now at the wastewater symposium! Come say hi if youβre here and talk about high accuracy
#longread
sequencing for
#microbial
,
#microbiome
, and
#metagenomics
.
@pacbio.bsky.social
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Rasmus Kirkegaard
Joe Hanson
5 months ago
I am calling for a complete and total boycott of the Mercator projection in all news stories about Greenland until every member of the American public has seen this
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Been doing a lot of
@nanoporetech.com
sequencing for soil and sediment lately and it appears that no matter how much DNA or how little we still get decent yields. So pretty robust performance. Yield clearly depends on pore count.
5 months ago
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Anyone gotten their hands on something crazy? Nvidia B200 or B300?
add a skeleton here at some point
5 months ago
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Rasmus Kirkegaard
Alex Loy
6 months ago
π’ 20 postdoctoral positions (full-time, 4 years) for outstanding female scientists π©βπ¬ π¬
@univie.ac.at
The E-STEEM programme call opens January 7th, 2026 and closes March 3rd, 2026.
careers.univie.ac.at/en/postdoc/e...
I participate as a host...
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https://careers.univie.ac.at/en/postdoc/e-steem
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The
@nanoporetech.com
π forgot the wrapping paper ππ
6 months ago
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One flowcell from
@nanoporetech.com
yielded 260 Gbp πππ€―π©
6 months ago
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Imagine sequencing the DNA of an entire country. Many colleagues have worked for years to sequence the DNA of soil and sediment samples covering Denmark to characterise the Danish microbial diversity π§¬πππ€―
add a skeleton here at some point
6 months ago
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Steven Robbins
7 months ago
Metagenomics colleagues! I'm looking for studies where both Illumina and ONT sequencing were performed on the same samples from soil, human, ruminent, and other sample types for comparison. Bonus if those studies include PacBio data. Please help and share!
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Dan Portik
7 months ago
Revio is a great product - it dramatically increased throughput over Sequel II (3x more data per cell, 12x more data per fully loaded run) and dropped the cost substantially. It's been the most successful instrument launch for the company, and now PacBio sequencing is at an all time high.
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Beating our previous record by a wide margin I asked myself "Are
@nanoporetech.com
flowcells getting better?" ππ©π§¬ Let's find out! I created a form where you can register your yields so we can get a better overview.
github.com/Kirk3gaard/O...
add a skeleton here at some point
7 months ago
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Did not expect to see disk space become an issue but after a disk clean up and restart I ended up with 243 and 244 gbp for these two
@nanoporetech.com
flowcells ππ𧬠ππ©ππ©ππ©
7 months ago
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After a day with almost 30 participants in the lab for our hands on
@nanoporetech.com
metagenomics course it is a blessing to see π©π©π©π©π©π©π©π©π©
7 months ago
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