Rasmus Kirkegaard
@kirk3gaard.bsky.social
Staff scientist having fun with DNA seq and bioinformatics at #AlbertsenLAB
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?
Value of DNA sequencing companies dropping faster than the price per genome?
February 11, 2025 at 11:56 AM
Value of DNA sequencing companies dropping faster than the price per genome?
"Tesla sales dropped 60% in Germany"
electrek.co/2025/02/05/t...
electrek.co/2025/02/05/t...
February 7, 2025 at 8:40 AM
"Tesla sales dropped 60% in Germany"
electrek.co/2025/02/05/t...
electrek.co/2025/02/05/t...
Did bulk options beyond 32 flowcells magically disappear @nanoporetech.com ?
February 7, 2025 at 8:35 AM
Did bulk options beyond 32 flowcells magically disappear @nanoporetech.com ?
Looking forward to see how much faster the nvidia RTX5090s will be at basecalling @nanoporetech.com data. Here SUP v5.0.0 with dorado 0.9.1 and the cards that we have available.
February 4, 2025 at 8:05 AM
Looking forward to see how much faster the nvidia RTX5090s will be at basecalling @nanoporetech.com data. Here SUP v5.0.0 with dorado 0.9.1 and the cards that we have available.
Just unboxed a new @nanoporetech.com P2S. Somehow the ONT logo has moved since the first one we got. 🟩🟩🟩🟩🟩🟩🟩
January 23, 2025 at 2:22 PM
Just unboxed a new @nanoporetech.com P2S. Somehow the ONT logo has moved since the first one we got. 🟩🟩🟩🟩🟩🟩🟩
Anyone have a cheap and easy to use lab solution for keeping track of reagent usage by users to support splitting bills for a multi PI lab? I am thinking scan a QR code on the cupbourd and type the number of reactions of e.g. Qubit, powersoil Pro you take.
December 13, 2024 at 1:04 PM
Anyone have a cheap and easy to use lab solution for keeping track of reagent usage by users to support splitting bills for a multi PI lab? I am thinking scan a QR code on the cupbourd and type the number of reactions of e.g. Qubit, powersoil Pro you take.
Putting this post on a t-shirt ;)
December 5, 2024 at 9:49 AM
Putting this post on a t-shirt ;)