Rasmus Kirkegaard
@kirk3gaard.bsky.social
Staff scientist having fun with DNA seq and bioinformatics at #AlbertsenLAB
Pinned
Rasmus Kirkegaard
@kirk3gaard.bsky.social
· Mar 21
GitHub - Kirk3gaard/MicroBench: Overview of our data for microbial genomic benchmarking
Overview of our data for microbial genomic benchmarking - Kirk3gaard/MicroBench
github.com
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.
@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.
The sun brings out the green @nanoporetech.com 🟩🟩🟩🟩🟩🚀🧬
Happy Friday everyone.
Happy Friday everyone.
February 13, 2026 at 4:02 PM
The sun brings out the green @nanoporetech.com 🟩🟩🟩🟩🟩🚀🧬
Happy Friday everyone.
Happy Friday everyone.
Reposted by Rasmus Kirkegaard
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...
apnews.com/article/mode...
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.
apnews.com
February 11, 2026 at 12:13 AM
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...
apnews.com/article/mode...
Reposted by Rasmus Kirkegaard
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
me: did you reverse complement the genome sequence?
claude: i'm a dumbass
February 7, 2026 at 8:59 AM
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
me: did you reverse complement the genome sequence?
claude: i'm a dumbass
Reposted by Rasmus Kirkegaard
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
February 5, 2026 at 5:12 PM
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
Reposted by Rasmus Kirkegaard
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...
www.nature.com/articles/s41...
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.
www.nature.com
January 28, 2026 at 9:41 PM
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...
www.nature.com/articles/s41...
Reposted by Rasmus Kirkegaard
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...)
January 21, 2026 at 5:43 PM
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...)
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...
January 19, 2026 at 7:44 PM
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...
Reposted by Rasmus Kirkegaard
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
January 15, 2026 at 5:31 PM
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
Reposted by Rasmus Kirkegaard
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
January 13, 2026 at 5:32 PM
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
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.
January 13, 2026 at 2:40 PM
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.
Anyone gotten their hands on something crazy? Nvidia B200 or B300?
@kirk3gaard.bsky.social , who wants to benchmark @nanoporetech.com 's Dorado with a Nvidia 5090 drawing 2500W? "MSI made a 2500W limited-edition RTX 5090 with a screen, because why not?"
MSI made a 2500W limited-edition RTX 5090 with a screen, because why not?
Make way for a limited edition GPU.
share.google
January 8, 2026 at 10:00 PM
Anyone gotten their hands on something crazy? Nvidia B200 or B300?
Reposted by Rasmus Kirkegaard
📢 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...
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...
careers.univie.ac.at
December 16, 2025 at 12:56 PM
📢 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...
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...
The @nanoporetech.com 🎅 forgot the wrapping paper 🎄🎁
December 10, 2025 at 12:39 PM
The @nanoporetech.com 🎅 forgot the wrapping paper 🎄🎁
One flowcell from @nanoporetech.com yielded 260 Gbp 🎉🚀🤯🟩
December 8, 2025 at 4:04 PM
One flowcell from @nanoporetech.com yielded 260 Gbp 🎉🚀🤯🟩
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 🧬🚀🎉🤯
New in @nature.com: The "Microflora Danica" project analyzed 10k+ samples to map Denmark's microbial life. Led by @aau.dk, Michael Wagner @michiwagner4.bsky.social, Daan Speth @daanspeth.bsky.social, Andrew Giguere @cemess.bsky.social @univie.ac.at analyzed nitrifiers.
December 3, 2025 at 8:52 PM
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 🧬🚀🎉🤯
Reposted by Rasmus Kirkegaard
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!
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!
November 11, 2025 at 8:21 PM
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!
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!
Reposted by Rasmus Kirkegaard
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.
November 5, 2025 at 5:59 PM
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.
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...
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...
November 5, 2025 at 9:10 AM
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...
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...
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 🎉🚀🧬 💚🟩💚🟩💚🟩
November 4, 2025 at 12:10 PM
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 🎉🚀🧬 💚🟩💚🟩💚🟩
After a day with almost 30 participants in the lab for our hands on @nanoporetech.com metagenomics course it is a blessing to see 🟩🟩🟩🟩🟩🟩🟩🟩🟩
November 3, 2025 at 4:26 PM
After a day with almost 30 participants in the lab for our hands on @nanoporetech.com metagenomics course it is a blessing to see 🟩🟩🟩🟩🟩🟩🟩🟩🟩
Reposted by Rasmus Kirkegaard
@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.
November 3, 2025 at 11:54 AM
@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.
Reposted by Rasmus Kirkegaard
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.
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.
October 22, 2025 at 10:36 AM
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.
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.
Anyone else seeing @nanoporetech.com flowcells starting to "die" exactly around 72 hours? Could this be voltage control not being optimised for longer durations?
October 21, 2025 at 7:23 AM
Anyone else seeing @nanoporetech.com flowcells starting to "die" exactly around 72 hours? Could this be voltage control not being optimised for longer durations?
Reposted by Rasmus Kirkegaard
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.
Comparison of picolyl azide-based BONCAT and microautoradiography for assessing the heterotrophic prokaryotic activity in the deep ocean www.biorxiv.org/content/10.1... #jcampubs 🌊
October 21, 2025 at 4:38 AM
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.