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.
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
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.
How I like my @nanoporetech.com runs 🟩💚🟩🚀🧬
October 20, 2025 at 6:15 PM
How I like my @nanoporetech.com runs 🟩💚🟩🚀🧬
Reposted by Rasmus Kirkegaard
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!
Postdoctoral position on methanotrophic bacteria - Vacancy at Aarhus University
Vacancy at Department of Biology - Microbiology, Aarhus University
international.au.dk
October 8, 2025 at 4:59 PM
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!
You load one @nanoporetech.com flowcell and it almost ruins your day 💩💩💩. You load six more and they look stunning 🟩💚🟩💚💚🟩
October 7, 2025 at 5:10 PM
You load one @nanoporetech.com flowcell and it almost ruins your day 💩💩💩. You load six more and they look stunning 🟩💚🟩💚💚🟩
Reposted by Rasmus Kirkegaard
Still 10 days left to apply! 🦠🧪👩🎓🔬
Come work with my team in beautiful Vienna!
Come work with my team in beautiful Vienna!
🚨3-yr Postdoc Position on #SingleCell Activities in #Marine #N-Cycling🦠🧪👩🎓🔬
Join me @univie.ac.at @dome-vienna.bsky.social
Part of our ERC Synergy #RECLESS looking at microbes in marine oxygen minimum zones
Apply by Oct 15, start March 2026!
-> ucloud.univie.ac.at/index.php/s/...
Join me @univie.ac.at @dome-vienna.bsky.social
Part of our ERC Synergy #RECLESS looking at microbes in marine oxygen minimum zones
Apply by Oct 15, start March 2026!
-> ucloud.univie.ac.at/index.php/s/...
RECLESS_Postdoc_single_cell_UniVie.pdf
u:cloud - Ihre Daten, auf Wolken gebettet.
ucloud.univie.ac.at
October 5, 2025 at 2:29 PM
Still 10 days left to apply! 🦠🧪👩🎓🔬
Come work with my team in beautiful Vienna!
Come work with my team in beautiful Vienna!
Reposted by Rasmus Kirkegaard
208Gb and can't tell you because it was for a customer
@timdepooter.bsky.social
@timdepooter.bsky.social
October 1, 2025 at 1:21 PM
208Gb and can't tell you because it was for a customer
@timdepooter.bsky.social
@timdepooter.bsky.social
Reposted by Rasmus Kirkegaard
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
October 1, 2025 at 1:34 PM
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
Reposted by Rasmus Kirkegaard
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...
duunitori.fi/tyopaikat/ty...
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!
duunitori.fi
September 30, 2025 at 8:37 AM
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...
duunitori.fi/tyopaikat/ty...
Reposted by Rasmus Kirkegaard
193-200Gbp without any washing step (sewer biofilms & soil enrichments) ❇️🚀
September 28, 2025 at 6:35 AM
193-200Gbp without any washing step (sewer biofilms & soil enrichments) ❇️🚀
Reposted by Rasmus Kirkegaard
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!
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!
September 27, 2025 at 2:49 AM
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!
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!
What is your highest yield on a @nanoporetech.com flowcell? And what was the sample type?
September 27, 2025 at 6:55 AM
What is your highest yield on a @nanoporetech.com flowcell? And what was the sample type?
Reposted by Rasmus Kirkegaard
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...
www.nature.com/articles/s41...
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%.
www.nature.com
August 14, 2025 at 11:01 PM
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...
www.nature.com/articles/s41...
Have not done much @nanoporetech.com sequencing lately but this looks pretty 🟩🟩🟩🟩🟩🟩 #MFDExtreme
June 24, 2025 at 3:27 PM
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?
June 24, 2025 at 2:49 PM
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
June 21, 2025 at 7:43 AM
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
Reposted by Rasmus Kirkegaard
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
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
So happy to read these @cemess.bsky.social news. Our centre at @univie.ac.at is really well positioned for future developments
@kathikitzinger.bsky.social
#MichaelZumstein
🧪 #Microsky
@kathikitzinger.bsky.social
#MichaelZumstein
🧪 #Microsky
June 19, 2025 at 10:37 AM
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
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
Reposted by Rasmus Kirkegaard
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...
Please see the official job ad here, and spread the word:
jobs.awi.de/Vacancies/20...
PostDoc in ecology and evolution of plasmids in polar waters at HIFMB (f/d/m)
Layout AWI HIPP extern, englisch
jobs.awi.de
June 5, 2025 at 8:09 AM
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...
Please see the official job ad here, and spread the word:
jobs.awi.de/Vacancies/20...