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Rasmus Kirkegaard @kirk3gaard.bsky.social · 22/06/2026

I wonder if @nanoporetech.com will ever release the much faster native barcoding kit where the sequencing adapters simply have the barcodes included. Surely those 75 minutes extra could save a life one day (+ minimize DNA loss and lab frustrations)

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Rasmus Kirkegaard @kirk3gaard.bsky.social · 11/06/2026

Great post as always 😁 Happy to see that your conclusion aligns with our experience even though we all hoped for HAC to deliver speed+consensus accuracy.

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Ryan Wick @rrwick.bsky.social · 11/06/2026

New blog post! I analyse the new hac@v6.0.0 basecalling model from @nanoporetech.com and discuss the conspicuous lack of a new sup model: rrwick.github.io/2026/06/11/d...

rrwick.github.io

Dorado v2.0.0: no more sup?

a blog for miscellaneous bioinformatics stuff

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Rasmus Kirkegaard @kirk3gaard.bsky.social · 08/06/2026

Is @nanoporetech.com hac v6 better than 5.2.0 sup? The short answer is no. But are a few errors in a genome worth 5 times more basecalling compute? github.com/Kirk3gaard/M...

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Oxford Nanopore @nanoporetech.com · 08/06/2026

Without trusted references, methylation data is hard to interpret. Using ATCC Genome Portal resources and nanopore sequencing, this webinar shows how to turn raw microbial modification signals into biological insight. bit.ly/4o369uU

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Steven Robbins @stevenjrobbins.bsky.social · 05/06/2026

It's also a boon for service providers with proms and high throughput. Many users can't/don't rebasecall and running sup on-machine limited the # of flow cells that could be run. v6 hac model means that more flow cells can be run concurrently to provide Q23 data directly for clients to run with.

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Jean P. Elbers @jpelbers.bsky.social · 05/06/2026

Hac 6.0.0 seems like a mixed bag to me compared to sup 5.2.0 based on github.com/Kirk3gaard/M... . Thanks for your hard work @kirk3gaard.bsky.social

github.com

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Steven Robbins @stevenjrobbins.bsky.social · 04/06/2026

Thought i'd highlight that the ONT London Calling tech talk is now up. Points of interest for the microbiome community: 1) Direct RNA multiplexing now available. Can now run 24 samples per flow cell, recover full-length transcripts with 8 base pair modifications... www.youtube.com/watch?v=CE69...

youtube.com

London Calling 2026 Technology update

YouTube video by Oxford Nanopore Technologies

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Heng Li @lh3lh3.bsky.social · 30/05/2026

Jeremy Wang developed rammap, a minimap2 rewrite in Rust. It achieves comparable or better performance than minimap2 and produces identical output to minimap2. During rewrite, Jeremy found two long-existing bugs in minimap2 which are fixed in v2.31. www.biorxiv.org/content/10.6...

biorxiv.org

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Rasmus Kirkegaard @kirk3gaard.bsky.social · 30/05/2026

For many years you needed UMIs and similar dark molecular biology magic to get perfect amplicon sequences from @nanoporetech.com data. With recent accuracy improvements+really clever algorithms that is now changed. Savont unlocks ASVs from low coverage nanopore amplicon data 🤯🤯🤯

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Human Pangenome Reference Consortium @humanpangenome.bsky.social · 26/05/2026

Abstract submissions for the T2T Face-to-Face conference are open through June 15th! Join the community Sept. 3–4 in Santa Cruz, CA, for two days of discussion and collaboration around telomere-to-telomere genomics and pangenomics. Learn more: sites.google.com/ucsc.edu/t2t...

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Rasmus Kirkegaard @kirk3gaard.bsky.social · 22/05/2026

Yes. Dorado just failed on the first try. Will look into basecalling next week 😁

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Rasmus Kirkegaard @kirk3gaard.bsky.social · 22/05/2026

SUP for now. Still have not had the time to benchmark hac 6.0.0 yet. Easier for big ongoing projects to stay with one model. A big miss that v6 is not launching in minknow already if it really is that good it would be great to be able to basecall 5 times more flowcells live 😁

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Rasmus Kirkegaard @kirk3gaard.bsky.social · 22/05/2026

When you run out of slots on the P24 it is handy to have a bunch of P2 solos 🟩🟩🧬 @nanoporetech.com

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Josh Quick @scalene.bsky.social · 22/05/2026

New preprint from us! 🦠 Clinical metagenomics is great for sequencing pathogens directly from patient samples but for some protocols sensitivity for RNA viruses lags behind bacteria & fungi. We have shown why, and how to fix it. www.medrxiv.org/content/10.6...

medrxiv.org

Library preparation strategy critically impacts RNA virus sensitivity in clinical metagenomics

Clinical metagenomics uses sequencing for culture-independent identification of pathogens directly from clinical specimens. While a number of protocols claim to be pathogen agnostic, sensitivity for R...

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Rasmus Kirkegaard @kirk3gaard.bsky.social · 15/05/2026

On this day in 2015 a disruptive company handed out DNA sequencers in goodie bags 🤯🤯🤯. Next week @nanoporetech.com is hosting their yearly London Calling event. Bring back disruption 🧬🚀

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Rasmus Kirkegaard @kirk3gaard.bsky.social · 11/05/2026

The nvidia dgx spark is a cool box but you get more @nanoporetech.com basecalling for your money with one of the other options (github.com/Kirk3gaard/2...)

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Rasmus Kirkegaard @kirk3gaard.bsky.social · 06/05/2026

Ever wondered what microbes you could find in Denmark? Pupils from Danish schools collected soil samples across the country so you can now browse the microbes (cmc-aau.github.io/masseeksperi...).

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Rasmus Kirkegaard @kirk3gaard.bsky.social · 04/05/2026

Will we see a new flowcell with even more pores for faster results?

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bioRxivpreprint @biorxivpreprint.bsky.social · 01/05/2026

Performance Test of the QNome Nanopore Sequencer www.biorxiv.org/content/10.64898/20…

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Rasmus Kirkegaard @kirk3gaard.bsky.social · 01/05/2026

Similar situation in academia when the professors "win money" to the university 🤣

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Rasmus Kirkegaard @kirk3gaard.bsky.social · 30/04/2026

Anyone happen to have a dgx spark doing nothing? Benchmark it for @nanoporetech.com basecalling (github.com/Kirk3gaard/2...)

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Rasmus Kirkegaard @kirk3gaard.bsky.social · 23/04/2026

And fast5 was discontinued long ago... Why is there any legacy code for that at all? 🤯

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Rasmus Kirkegaard @kirk3gaard.bsky.social · 23/04/2026

Why would @nanoporetech.com minknow produce fast5 files in 2026???

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Rasmus Kirkegaard @kirk3gaard.bsky.social · 19/04/2026

More do it at home @nanoporetech.com sequencing is being announced on X (x.com/SethSHowes/s...) A blog post by Seth Howes (iwantosequencemygenomeathome.com). Hope London Calling will feature a tinkerer session this year.

x.com

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Rasmus Kirkegaard @kirk3gaard.bsky.social · 15/04/2026

2 cents will not buy you useful amounts of data yet 😉

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Steven Robbins @stevenjrobbins.bsky.social · 14/04/2026

There's a reason why most undiscovered taxa come from soils, sediments, wetlands, etc: www.nature.com/articles/s41... The way I prefer to think about it is to put that money into long reads and get usable data.

nature.com

Unbinned contigs expand known diversity in the global microbiome - Nature Microbiology

Re-analysis of over 92,000 metagenomes reveals hundreds of thousands of previously undescribed Bacterial and Archaeal clades hidden in plain sight.

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Rasmus Kirkegaard @kirk3gaard.bsky.social · 14/04/2026

For soil and sediment we do one sample per flowcell. The complexity of these sample types is fairly high for simpler communities barcoding is a good option.

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Earth BioGenome Project 🌍 @ebpgenome.bsky.social · 13/04/2026

A major milestone for biodiversity genomics: EBP-affiliated projects have now contributed over 6,000 genome assemblies toward the goal of sequencing all known eukaryotic life. 🧬 Thank you to all EBP-affiliated projects behind this work, from sampling and DNA extraction to sequencing and assembly.

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Rasmus Kirkegaard @kirk3gaard.bsky.social · 13/04/2026

Yeah with the powermax you get enough to afford doing the pre prep cleanups + the LSK114 goes well even with low amounts of dna loaded onto the flowcell. Think we maxed out pore occupancy down to roughly 20 ng loaded.

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Rasmus Kirkegaard @kirk3gaard.bsky.social · 13/04/2026

Quite a few flowcells going beyond 200 gbp

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Rasmus Kirkegaard @kirk3gaard.bsky.social · 13/04/2026

Our samples include sediment, soil, sand etc. Power max kit + SPRI cleanup before the LSK prep.

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Rasmus Kirkegaard @kirk3gaard.bsky.social · 13/04/2026

We have received 200+ on several flowcells. Think the record was 260 gbp (estimated).

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Rasmus Kirkegaard @kirk3gaard.bsky.social · 09/04/2026

Our median nanopore yield is around 170 gbp. We see flowcells going beyond 200 gbp quite often.

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Shuai Wang @wshuai.bsky.social · 31/03/2026

Our ECE-host framework doesn't care which sequencing platform you use—it’s ready to go once you have mod calling results. The kicker is that we need scalable mod calling from metagenomics. If it doesn't scale, the ECE-host analysis can't happen.

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The Banfield Lab @banfieldlab.bsky.social · 30/03/2026

Congratulations @wshuai.bsky.social and co-authors! We’re excited to introduce MODIFI, our new scalable method for detecting DNA modifications in PacBio metagenomic data and estimating ECE-host linkage. Check out the preprint: www.biorxiv.org/content/10.6...

biorxiv.org

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Rasmus Kirkegaard @kirk3gaard.bsky.social · 28/03/2026

Demand for ai generated cat videos etc 📈

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Rasmus Kirkegaard @kirk3gaard.bsky.social · 28/03/2026

Will be even more by Monday 🤣 Our IT team told us that now is a bad time to buy hardware... Orders already placed get cancelled due to price hikes or delivery issues. I fear that we are just seeing the beginning and now will turn out to have been a bargain a year from now 🤣

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Jim Shaw @jimshaw.bsky.social · 24/03/2026

_720 Gbp_ marine nanopore metagenome -> 328 circular prokaryotic contigs: using myloasm! Insane work by Lui and Nielsen. Also shows how modern long read assemblies can disentangle coexisting strains and reveal ecological insights.

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Rasmus Kirkegaard @kirk3gaard.bsky.social · 20/03/2026

Will 2026 be the year we finally see something new from @nanoporetech.com or are we stuck due to the clinical focus? Next generation ASIC chips would be the opportunity to align product lines. One flowcell to rule them all?

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Morten Kam Dahl Dueholm @mkddueholm.bsky.social · 02/03/2026

A new era for #ONT amplicon sequencing? We show that #ONT #amplicon sequencing now achieves accuracy sufficient for #ASV resolution using standard Illumina-based pipelines. We validated this by sequencing identical amplicons on #ONT and #PacBio. @nanoporetech.com www.biorxiv.org/content/10.6...

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Rasmus Kirkegaard @kirk3gaard.bsky.social · 13/02/2026

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

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Edward Nirenberg @enirenberg.bsky.social · 11/02/2026

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

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.

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James Ferguson @psy-fer.bsky.social · 07/02/2026

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

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Oxford Nanopore @nanoporetech.com · 05/02/2026

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. bit.ly/4awzU15

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Rasmus Kirkegaard @kirk3gaard.bsky.social · 31/01/2026

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

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