Rasmus Kirkegaard

The sun brings out the green @nanoporetech.com 🟩🟩🟩🟩🟩🚀🧬
Happy Friday everyone.

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.

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...

Hey @bsky.app can we get a poll option?

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

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

En anden ting er effektiviteten af bilen. Hvor mange km/min tilføjer man 😁⚡🚗

When you look up something and all the links are already purple 😉

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.

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...

GitHub - bluenote-1577/sylph: ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash. ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash. - bluenote-1577/sylph

Well we still mostly run denovo assembly of everything. But people like sylph for speedy classification of reads github.com/bluenote-157...

Which assembler do you use?

alignment of reads to reference genome. a poly-t region was created by a single read in the dataset.

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...)

Makes sense with the many mods still to be covered in RNA. How much data do you get from RNA runs these days?

Yeah we go SUP+mods on everything

We basecall with modification calls and consider uploading just the bam. The added benefit of raw data is limited and cannot justify the storage needs?

The workaround is to pack Pod5 and fastq in on tar.gz and upload that as nanopore rawdata. It is not pretty but it works. However, I am not sure storing Pod5 is worth it.

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...

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

Pore occupancy is generally high to get to these yield numbers.

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

Yes. These are metagenomic samples after bead beating so pretty much the sweet spot for sequencing.

These are powermax +lfb cleanup before doing regular lsk preps. Sediments have been doing great for us.

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.

Yeah I expect that most of them are busy making cat videos but hopefully some of them will be available for science

Anyone gotten their hands on something crazy? Nvidia B200 or B300?

📢 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 @nanoporetech.com 🎅 forgot the wrapping paper 🎄🎁

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 🧬🚀🎉🤯

Removes fragments below 3 kbp. So slightly more size selection compared to just ethanol.