Rasmus Kirkegaard
@kirk3gaard.bsky.social
๐ค 491
๐ฅ 258
๐ 129
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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Why would
@nanoporetech.com
minknow produce fast5 files in 2026???
7 days 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
11 days ago
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Rasmus Kirkegaard
Steven Robbins
16 days 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 ๐
17 days 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. ๐งฌ 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
about 1 month ago
Our ECE-host framework doesn't care which sequencing platform you useโitโs 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
about 1 month ago
Congratulations
@wshuai.bsky.social
and co-authors! Weโre 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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Rasmus Kirkegaard
Jean P. Elbers
about 1 month 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 Intelโs 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
about 1 month 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
about 1 month ago
ElysION Fields
omicsomics.blogspot.com/2026/03/elys...
๐งฌ๐ฅ๏ธ
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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?
about 1 month ago
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Rasmus Kirkegaard
Morten Kam Dahl Dueholm
about 2 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
๐ฉ๐ฉ๐ฉ๐ฉ๐ฉ๐๐งฌ Happy Friday everyone.
3 months ago
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Rasmus Kirkegaard
Edward Nirenberg
3 months ago
It is absolutely outrageous that Modernaโs flu vaccine was met with a โrefusal-to-fileโ 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 Modernaโs 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?
3 months ago
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Rasmus Kirkegaard
James Ferguson
3 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
3 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
3 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
3 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...
3 months ago
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Rasmus Kirkegaard
Jeremy Wilkinson
3 months ago
Iโm now at the wastewater symposium! Come say hi if youโre here and talk about high accuracy
#longread
sequencing for
#microbial
,
#microbiome
, and
#metagenomics
.
@pacbio.bsky.social
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Rasmus Kirkegaard
Joe Hanson
4 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.
4 months ago
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Anyone gotten their hands on something crazy? Nvidia B200 or B300?
add a skeleton here at some point
4 months ago
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Rasmus Kirkegaard
Alex Loy
5 months ago
๐ข 20 postdoctoral positions (full-time, 4 years) for outstanding female scientists ๐ฉโ๐ฌ ๐ฌ
@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
๐ forgot the wrapping paper ๐๐
5 months ago
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One flowcell from
@nanoporetech.com
yielded 260 Gbp ๐๐๐คฏ๐ฉ
5 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 ๐งฌ๐๐๐คฏ
add a skeleton here at some point
5 months ago
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Rasmus Kirkegaard
Steven Robbins
6 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
6 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?" ๐๐ฉ๐งฌ 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
6 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 ๐๐๐งฌ ๐๐ฉ๐๐ฉ๐๐ฉ
6 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 ๐ฉ๐ฉ๐ฉ๐ฉ๐ฉ๐ฉ๐ฉ๐ฉ๐ฉ
6 months ago
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Rasmus Kirkegaard
Albert Vilella, PhD.
6 months ago
@kirk3gaard.bsky.social
, not recently active on Bluesky, on the 'tech bro' backing of Oxford
@nanoporetech.com
. We kind of already have a
#techbro
backing ONT,
#LarryEllis
who is one of the main investors and has put a ton of money into Oxford's EIT.
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Rasmus Kirkegaard
A. Murat Eren (Meren)
6 months ago
Please share this with anyone who may be interested in a post-doc in Germany:
jobs.awi.de/Vacancies/20...
This is quite an exciting opportunity to push the boundaries of what is known regarding the molecular basis of the formation and demise of photosymbiotic relationships in marine habitats.
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Anyone else seeing
@nanoporetech.com
flowcells starting to "die" exactly around 72 hours? Could this be voltage control not being optimised for longer durations?
6 months ago
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Rasmus Kirkegaard
Roland Hatzenpichler
6 months ago
Preprint: Comparing BONCAT and MAR. Pro tips: don't buy the ClickIT kit, it's 25x overpriced as compared to buying individual chemicals by themselves (see my 2015 protocol chapter) and making reagents fresh gives superior results. And yes, only use picolyl dyes, my lab has been doing so since 2018.
add a skeleton here at some point
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How I like my
@nanoporetech.com
runs ๐ฉ๐๐ฉ๐๐งฌ
6 months ago
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Rasmus Kirkegaard
Ian Marshall
7 months ago
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
!
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Postdoctoral position on methanotrophic bacteria - Vacancy at Aarhus University
Vacancy at Department of Biology - Microbiology, Aarhus University
https://international.au.dk/about/profile/vacant-positions/job/postdoctoral-position-on-methanotrophic-bacteria
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You load one
@nanoporetech.com
flowcell and it almost ruins your day ๐ฉ๐ฉ๐ฉ. You load six more and they look stunning ๐ฉ๐๐ฉ๐๐๐ฉ
7 months ago
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Rasmus Kirkegaard
Kathi Kitzinger
7 months ago
Still 10 days left to apply! ๐ฆ ๐งช๐ฉโ๐๐ฌ Come work with my team in beautiful Vienna!
add a skeleton here at some point
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Rasmus Kirkegaard
Wouter De Coster
7 months ago
208Gb and can't tell you because it was for a customer
@timdepooter.bsky.social
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Rasmus Kirkegaard
Tim De Pooter
7 months ago
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
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Rasmus Kirkegaard
Teppo Hiltunen
7 months ago
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...
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Professor or Associate professor (Tenure Track/Full) in Microbial Genetics of Health - Turun yliopisto - Tyรถpaikat - Duunitori
Avoin tyรถpaikka: Professor or Associate professor (Tenure Track/Full) in Microbial Genetics of Health - Turun yliopisto, Turku. Duunitorilla lisรคksi yli 30 000 muuta avointa tyรถpaikkaa. Lue lisรครค nyt!
https://duunitori.fi/tyopaikat/tyo/professor-or-associate-professor-tenure-trackfull-in-microbial-genetics-of-health-stsur-19627560
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Rasmus Kirkegaard
7 months ago
193-200Gbp without any washing step (sewer biofilms & soil enrichments) โ๏ธ๐
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Rasmus Kirkegaard
Alex Crits-Christoph
7 months ago
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!
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What is your highest yield on a
@nanoporetech.com
flowcell? And what was the sample type?
7 months ago
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Steven Robbins
9 months ago
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...
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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%.
https://www.nature.com/articles/s41564-025-02062-z
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Have not done much
@nanoporetech.com
sequencing lately but this looks pretty ๐ฉ๐ฉ๐ฉ๐ฉ๐ฉ๐ฉ
#MFDExtreme
10 months ago
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Gotta catch em all! A little late night sampling for the MFD Extreme project. What microbes call this sand their home?
10 months ago
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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 ๐๐ฆ ๐งฌ๐ฉ๐ฐ
#MFDExtreme
10 months ago
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