This will make indexing k-mers in e.g. HPRC (human) and GTDB (bacteria) a breeze

Ragnar {Groot Koerkamp}@curiouscoding.nl · 5d ago

I've been working on Pandedup the past weeks: a tool to quickly dedup the k-mer content of a pangenome (read: HPRCv2). Just uploaded a k=64 SPSS (k-mer spectrum preserving string set) as well: zenodo.org/records/2172... This reduces the ~1.5Tbp input to just 10.6Gbp. github.com/RagnarGrootK...

I've been working on Pandedup the past weeks: a tool to quickly dedup the k-mer content of a pangenome (read: HPRCv2). Just uploaded a k=64 SPSS (k-mer spectrum preserving string set) as well: zenodo.org/records/2172... This reduces the ~1.5Tbp input to just 10.6Gbp. github.com/RagnarGrootK...

GitHub - RagnarGrootKoerkamp/pandedup: Pandedup uses minimizers to build a quick & dirty k-mer spectrum (SPSS) from a .AGC pangenome.

Pandedup uses minimizers to build a quick & dirty k-mer spectrum (SPSS) from a .AGC pangenome. - RagnarGrootKoerkamp/pandedup

github.com

HPRC2: A human pangenome reference with near-complete coverage of common genetic variation https://www.biorxiv.org/content/10.64898/2026.07.21.739710v1

Also, Deacon was the motivation for engineering the k-PHF Hash Set! bsky.app/profile/curi...

Ragnar {Groot Koerkamp}@curiouscoding.nl · 4w ago

My secret 4th ALGO paper is out! We show a tight space lower on non-minimal k-perfect hash functions, generalize PtrHash into a non-minimal k-PHF, and then use it to develop a hash set implementation that is up to 1.6x faster than other hash sets! With Stefan {Hermann, Walzer} and Peter Sanders

My secret 4th ALGO paper is out! We show a tight space lower on non-minimal k-perfect hash functions, generalize PtrHash into a non-minimal k-PHF, and then use it to develop a hash set implementation that is up to 1.6x faster than other hash sets! With Stefan {Hermann, Walzer} and Peter Sanders

arXiv cs.DS Data Structures and Algorithms@csds-bot.bsky.social · 4w ago

Ragnar Groot Koerkamp, Stefan Hermann, Peter Sanders, Stefan Walzer: Non-minimal k-perfect hashing: Tight lower bounds and an application to fast static hash tables https://arxiv.org/abs/2607.07257 https://arxiv.org/pdf/2607.07257 https://arxiv.org/html/2607.07257

Preprint alert! arxiv.org/abs/2602.03525 TLDR: ZOR filters are STATIC filters with false positives. -Almost memory optimal: <1% overhead over the theoretical lower bound (!!!) -Fast queries: ~100 ns -Construction cannot fail A thread:

ZOR filters: fast and smaller than fuse filters

Probabilistic membership filters support fast approximate membership queries with a controlled false-positive probability $\varepsilon$ and are widely used across storage, analytics, networking, and b...

arxiv.org

Ever wanted to quickly check host content of DNA sequences? bede.im/sapiometer

139 genomes now sequenced from the ongoing 2026 Bundibugyo virus disease outbreak in DRC, spanning 16 Health Zones. Led by INRB with support from the ARTIC network (Wellcome Trust and Gates Foundation). Full analysis: virological.org/t/genomic-ep...

Genomic epidemiology of the ongoing 2026 Bundibugyo Virus Disease outbreak in the Democratic Republic of the Congo

Genomic epidemiology of the ongoing 2026 Bundibugyo Virus Disease outbreak in the Democratic Republic of the Congo Institut National de Recherche Biomédicale (INRB), Kinshasa – DRC and partners Conte...

virological.org

"You gather your most expensive people into a room to make your most important decisions. Then, somewhere in the second hour, the room quietly gets worse at making them. Not the people. The room."

Important read from ARTIC PI Placide Mbala (INRB) and @krutikakuppalli.bsky.social in @statnews.com, on what the Bundibugyo Ebola outbreak reveals about the limits of pathogen-specific diagnostics, and why we need pathogen-agnostic systems for the next emergency www.statnews.com/2026/07/01/e...

What Ebola and Marburg are teaching us about the next pandemic

“What is urgently needed is a shift from pathogen-specific diagnostics toward pathogen-agnostic diagnostic systems,” write Krutika Kuppalli and Placide Mbala.

statnews.com

Excellent update from @pathoplexus.org this month. Pathoplexus has been central to data sharing during the ongoing Bundibugyo ebolavirus outbreak response, with ARTIC contributing developer time to Loculus, the platform behind it.

Pathoplexus@pathoplexus.org · last mo.

1/ 🌍 Our June update is here! Two new pathogens added in response to active outbreaks, over 5,700 new sequences, and a growing community of labs from around the world. Here's what's new in #Pathoplexus 👇 Read the full update: pathoplexus.org/news/2026-06... 📰

Air conditioning is not ventilation. Crisp and dry conditioned air feels fresh but often isn't. Beware of this sensory trickery.

Are you a computational immunologist or bioinformatician interested in impactful vaccine research? We're hiring a postdoc to join @psioxford.bsky.social work in vaccine immunology and evaluation, working on the ChAdOx1 Nipah vaccine. Please get in touch! my.corehr.com/pls/uoxrecru...

🧬 New preprint! We clustered 5.6 million bacterial genomes into genomically cohesive units (GCUs) 500× faster than existing tools. (In just 14 hours, 16.5 GB RAM using 48 CPUs). 🦠🐙Meet gemsparcl 💎✨! www.biorxiv.org/content/10.6...

Emergency hospital admissions fell after introduction of London’s T-charge and Ulez, study suggests

Emergency hospital admissions fell after introduction of London’s T-charge and Ulez, study suggests

Imperial College scientists analysed health records before and after introduction of air pollution reduction zones Low emission and clean air zones attract controversy whenever they are proposed, but there is growing evidence that they work in improving air quality. The Bradford zone was followed by a reduction of about 25% in GP visits for heart and breathing problems and survey data shows that the central London zone was followed by a reduction in the likelihood of a person taking sick leave. Now analysis of health records has found emergency admissions to hospital reduced after the introduction of the T-charge and ultra-low emissions zone (Ulez) in central London. Continue reading...

theguardian.com

Never have I seen the car/road metaphor pushed this hard

Paving the way for agents in biology

Anthropic is an AI safety and research company that's working to build reliable, interpretable, and steerable AI systems.

anthropic.com

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...

"On-board Wi-Fi was also tested by Ofcom and it performed well just one percent of the time."

The Register@theregister.com · 2mo ago

Brit regulator finds mobile network service on trains is far from first class

#r4today @drtedros.who.int: "While investing in defence… Please don't forget the common enemy that we have: a virus that doesn't care about our borders, our politics, or about whatever excuses we have. We have to be also prepared for that." www.bbc.co.uk/sounds/play/...

Today - 05/06/2026 - BBC Sounds

News and current affairs, including Sports Desk, Weather and Thought for the Day.

bbc.co.uk

Now that Sassy had been published and presented, it's time for it to break out of my bubble :) curiouscoding.nl/posts/sassy/ www.reddit.com/r/rust/comme...

The ARTIC Primer Foundry is now live and will soon begin shipping BDBV primers on request primalscheme.com/orders

ARTIC network has published Bundibugyo (BDBV) sequencing resources as the 2026 outbreak continues in DRC & Uganda. We have compiled guidance for labs wishing to sequence, assemble and analyse BDBV genomes: artic.network/viruses/bdbv/bdbv-sequencing-guide.html

the FT has two pieces on the slow-motion collapse of UK higher ed. 4/5ths of unis are doing voluntary layoffs; 38% are doing compulsory. Meanwhile Britain and its flatlined productivity growth sleepwalks through its unprecedented loss of advanced capabilities www.ft.com/content/8097...

Memory-safe high-performance sequence mapping with rammap https://www.biorxiv.org/content/10.64898/2026.05.26.726289v1

This is awful to hear, describing how Sean Eddy (HMMER, infernal, pfam, rfam) has been defunded. The letter said his work "had been determined to be of absolutely no value to the US taxpayer, and therefore it was being specifically terminated," www.npr.org/2026/05/21/n...

Researchers say the Trump administration is finding new ways to punish science

Even with federal grants largely restored, scientists say the Trump administration is still preventing those funds from reaching them. The consequences, they say, are already becoming clear.

npr.org

My WABI submission: anti-lexicographic SUS-anchors. For sigma=4, this selection scheme (a k=1 sampling scheme) has density within 1% of the lower bound! The idea: find the smallest* substring that does not have a 2nd occurrence, and sample its start pos. curiouscoding.nl/posts/sus-an...

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...

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...

medrxiv.org

Widely used clinical metagenomics protocols exhibit low sensitivity for RNA viruses. In this preprint we show why this happens and how to fix it. www.medrxiv.org/content/10.6... @dominikaanna.bsky.social @scalene.bsky.social @pathogenomenick.bsky.social

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...

medrxiv.org

It's hard to imagine how a tragedy like Baby P happens until you witness child abuse in your community, report it, report it again, others report it, and yet year after year violence continues. Social services, landlord, council, police passing buck and appeasing. en.wikipedia.org/wiki/Killing...