Rasmus Kirkegaard
@kirk3gaard.bsky.social
📤 484
📥 256
📝 116
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
12 months ago
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reposted by
Rasmus Kirkegaard
Morten Kam Dahl Dueholm
6 days 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
🟩🟩🟩🟩🟩🚀🧬 Happy Friday everyone.
23 days ago
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Rasmus Kirkegaard
Edward Nirenberg
25 days ago
It is absolutely outrageous that Moderna’s flu vaccine was met with a “refusal-to-file” 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 Moderna’s 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?
27 days ago
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reposted by
Rasmus Kirkegaard
James Ferguson
29 days 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
about 1 month 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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Rasmus Kirkegaard
Dan Portik
about 1 month 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
about 2 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...
about 2 months ago
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Rasmus Kirkegaard
Jeremy Wilkinson
about 2 months ago
I’m now at the wastewater symposium! Come say hi if you’re here and talk about high accuracy
#longread
sequencing for
#microbial
,
#microbiome
, and
#metagenomics
.
@pacbio.bsky.social
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Rasmus Kirkegaard
Joe Hanson
about 2 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.
about 2 months ago
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Anyone gotten their hands on something crazy? Nvidia B200 or B300?
add a skeleton here at some point
about 2 months ago
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Rasmus Kirkegaard
Alex Loy
3 months ago
📢 20 postdoctoral positions (full-time, 4 years) for outstanding female scientists 👩🔬 🔬
@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
🎅 forgot the wrapping paper 🎄🎁
3 months ago
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One flowcell from
@nanoporetech.com
yielded 260 Gbp 🎉🚀🤯🟩
3 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 🧬🚀🎉🤯
add a skeleton here at some point
3 months ago
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Rasmus Kirkegaard
Steven Robbins
4 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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Rasmus Kirkegaard
Dan Portik
4 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?" 🚀🟩🧬 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
4 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 🎉🚀🧬 💚🟩💚🟩💚🟩
4 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 🟩🟩🟩🟩🟩🟩🟩🟩🟩
4 months ago
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reposted by
Rasmus Kirkegaard
Albert Vilella, PhD.
4 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)
5 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?
5 months ago
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Rasmus Kirkegaard
Roland Hatzenpichler
5 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 🟩💚🟩🚀🧬
5 months ago
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Rasmus Kirkegaard
Ian Marshall
5 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 💩💩💩. You load six more and they look stunning 🟩💚🟩💚💚🟩
5 months ago
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Rasmus Kirkegaard
Kathi Kitzinger
5 months ago
Still 10 days left to apply! 🦠🧪👩🎓🔬 Come work with my team in beautiful Vienna!
add a skeleton here at some point
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Rasmus Kirkegaard
Wouter De Coster
5 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
5 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
5 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 - 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!
https://duunitori.fi/tyopaikat/tyo/professor-or-associate-professor-tenure-trackfull-in-microbial-genetics-of-health-stsur-19627560
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reposted by
Rasmus Kirkegaard
5 months ago
193-200Gbp without any washing step (sewer biofilms & soil enrichments) ❇️🚀
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Rasmus Kirkegaard
Alex Crits-Christoph
5 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?
5 months ago
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Rasmus Kirkegaard
Steven Robbins
7 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 🟩🟩🟩🟩🟩🟩
#MFDExtreme
9 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?
9 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 🎉🦠🧬🇩🇰
#MFDExtreme
9 months ago
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Rasmus Kirkegaard
Kathi Kitzinger
9 months ago
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
add a skeleton here at some point
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Rasmus Kirkegaard
A. Murat Eren (Meren)
9 months ago
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...
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PostDoc in ecology and evolution of plasmids in polar waters at HIFMB (f/d/m)
Layout AWI HIPP extern, englisch
https://jobs.awi.de/Vacancies/2002/Description/2
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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 🎉
9 months ago
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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)
9 months ago
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Rasmus Kirkegaard
Alexander Price
9 months ago
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!
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Wandering while wondering if this sample cup will hold a story exciting enough for
@isme-microbes.bsky.social
conference in New Zealand next year 🦠
9 months ago
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Rasmus Kirkegaard
Ryan Wick
9 months ago
I tested myloasm on a 50x Klebsiella isolate, and it was very fast - only took about 1 minute to complete (on my Macbook).
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Rasmus Kirkegaard
Alex Crits-Christoph
9 months ago
Promising toolkit for binning and visualizing assembly graphs. The assembly graph is an underutilized source of binning information IMO
gbintk.readthedocs.io/en/latest/
add a skeleton here at some point
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Rasmus Kirkegaard
Jim Shaw
9 months ago
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)
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Rasmus Kirkegaard
Jim Shaw
9 months ago
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
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myloasm - metagenomic assembly with (noisy) long reads
https://myloasm-docs.github.io/
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