Rasmus Kirkegaard
@kirk3gaard.bsky.social
Staff scientist having fun with DNA seq and bioinformatics at #AlbertsenLAB
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.
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...
Yes. These are metagenomic samples after bead beating so pretty much the sweet spot for sequencing.
January 15, 2026 at 6:00 AM
Yes. These are metagenomic samples after bead beating so pretty much the sweet spot for sequencing.
I assume it depends on who is pouring the pores onto the flowcells at the factory (randomness).
January 13, 2026 at 4:55 PM
I assume it depends on who is pouring the pores onto the flowcells at the factory (randomness).
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.
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 🎉🚀🤯🟩
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 🟩🟩🟩🟩🟩🟩🟩🟩🟩
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?
How I like my @nanoporetech.com runs 🟩💚🟩🚀🧬
October 20, 2025 at 6:15 PM
How I like my @nanoporetech.com runs 🟩💚🟩🚀🧬
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 🟩💚🟩💚💚🟩
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
Quality scores seem to be pretty well calibrated but is a bit conservative which is probably better than being overly optimistic. Mappings with 100 % identity hits come from a wide range of quality scores
June 16, 2025 at 12:09 PM
Quality scores seem to be pretty well calibrated but is a bit conservative which is probably better than being overly optimistic. Mappings with 100 % identity hits come from a wide range of quality scores
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 🎉
June 6, 2025 at 11:55 AM
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 🎉
Even some pretty long reads in the 100 % identity pool.
June 4, 2025 at 1:55 PM
Even some pretty long reads in the 100 % identity pool.
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)
(Reads were mapped with minimap2 and identity scores from nanoplot were used for phred score calculations)
June 4, 2025 at 1:54 PM
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)
(Reads were mapped with minimap2 and identity scores from nanoplot were used for phred score calculations)
Wandering while wondering if this sample cup will hold a story exciting enough for @isme-microbes.bsky.social conference in New Zealand next year 🦠
May 30, 2025 at 6:48 AM
Wandering while wondering if this sample cup will hold a story exciting enough for @isme-microbes.bsky.social conference in New Zealand next year 🦠
Considering an apple gpu for your @nanoporetech.com basecalling? Then I hope you have lots of patience or is happy with "fast" mode data quality.
github.com/Kirk3gaard/2...
github.com/Kirk3gaard/2...
April 17, 2025 at 9:03 AM
Considering an apple gpu for your @nanoporetech.com basecalling? Then I hope you have lots of patience or is happy with "fast" mode data quality.
github.com/Kirk3gaard/2...
github.com/Kirk3gaard/2...
Already some nice entries added to the list for @nanoporetech.com basecalling 🎉 Do you have some nvidia GPUs that are missing?
April 10, 2025 at 1:55 PM
Already some nice entries added to the list for @nanoporetech.com basecalling 🎉 Do you have some nvidia GPUs that are missing?
Help your fellow researchers decide what nvidia GPU to buy for their @nanoporetech.com basecalling needs.
github.com/Kirk3gaard/2...
github.com/Kirk3gaard/2...
April 9, 2025 at 7:22 AM
Help your fellow researchers decide what nvidia GPU to buy for their @nanoporetech.com basecalling needs.
github.com/Kirk3gaard/2...
github.com/Kirk3gaard/2...
Okay. So I have not done the @nanoporetech.com native barcoding preps for some years. It went form including an ampure cleanup step and take forward 75 % of your DNA to no ("optional") cleanup and take forward 0.75/15ul=5 % of your DNA. Any inputs on whether yield performance is similar?
March 27, 2025 at 11:40 AM
Okay. So I have not done the @nanoporetech.com native barcoding preps for some years. It went form including an ampure cleanup step and take forward 75 % of your DNA to no ("optional") cleanup and take forward 0.75/15ul=5 % of your DNA. Any inputs on whether yield performance is similar?
After reading recent blog posts by
@omicsomics.bsky.social
with the development and history of DNA seq I realized that I was missing an updated figure to summarize it in the style originally by @lexnederbragt.bsky.social (flxlexblog.wordpress.com/2016/07/08/d...) Anyone doing a 2025 edition?
@omicsomics.bsky.social
with the development and history of DNA seq I realized that I was missing an updated figure to summarize it in the style originally by @lexnederbragt.bsky.social (flxlexblog.wordpress.com/2016/07/08/d...) Anyone doing a 2025 edition?
March 25, 2025 at 12:05 PM
After reading recent blog posts by
@omicsomics.bsky.social
with the development and history of DNA seq I realized that I was missing an updated figure to summarize it in the style originally by @lexnederbragt.bsky.social (flxlexblog.wordpress.com/2016/07/08/d...) Anyone doing a 2025 edition?
@omicsomics.bsky.social
with the development and history of DNA seq I realized that I was missing an updated figure to summarize it in the style originally by @lexnederbragt.bsky.social (flxlexblog.wordpress.com/2016/07/08/d...) Anyone doing a 2025 edition?