Curtis Kapsak

New blog post: ONT read QC strategies for assembly
rrwick.github.io/2026/02/05/r...

Mini-study comparing a few QC/subsampling approaches, plus practical notes from my experience.

Opinion | The CDC Shooting Isn't What Broke Me Continuing to show up to work at an agency I no longer trust is devastating

“We are grieving the realization that dedication alone cannot protect an agency from leaders determined to destroy it…. Still, CDC scientists will keep showing up. We will keep doing good science for as long as we are allowed to.”

covSPECTRUM covSPECTRUM is an interactive platform aiming to help scientists investigate and identify variants of SARS-CoV-2.

cov-spectrum.org/news/2025-12...

YouTube video by LastWeekTonight Bari Weiss: Last Week Tonight with John Oliver (HBO)

Hi.

Congrats @efosternyarko.bsky.social and team for this great work building capacity for public health genomics to investigate cholera and other enteric bacteria, across Africa 👏

www.lshtm.ac.uk/research/cen...

1/ 🚀 Exciting news: we’ve just released the first Nextclade dataset for Enterovirus D68 (EV-D68), developed in collaboration with the European Non-Polio Enterovirus Network (ENPEN).

👉🏻 Check out the dataset on Nextclade! clades.nextstrain.org?dataset-name...

#EVD68 #Enterovirus #OpenData

Please join us for the @who.int EPI-WIN webinar introducing WHO’s report on Attributes and Principles of Pathogen Genomic Data-Sharing Platforms. 24 November 2025, 1-2pm CET.
🔗 Register: who.zoom.us/webinar/regi...
👉 Webinar info: www.who.int/news-room/ev...
📄 Report: iris.who.int/bitstreams/f...

a drawing of two people with helmets and the word kino below them ALT: a drawing of two people with helmets and the word kino below them

did someone say steam machine?

Ecology and spread of the North American H5N1 epizootic - Nature The panzootic of highly pathogenic H5N1 since 2021 was driven by around nine introductions into the Atlantic and Pacific flyways, followed by rapid dissemination through wild migratory birds, primaril...

Our lab's paper describing the North American H5N1 epizootic is out now in Nature! So thrilled to have this out, and congratulations to @lambod50.bsky.social for all the fantastic work on this: www.nature.com/articles/s41...

First locally acquired U.S. cases of more severe mpox strain reported — CBS News California health officials have reported two cases of a potentially more severe form of mpox that appear to be locally acquired.

apple.news/AfbRCeaNOR_q...

RFK Jr. Promotes Natural Immunity With Invitation To Touch His Festering Sore

RFK Jr. Promotes Natural Immunity With Invitation To Touch His Festering Sore https://theonion.com/rfk-jr-promotes-natural-immunity-with-invitation-to-touch-his-festering-sore/

Thanks for sharing! We're super excited we could play a role in this project. Wastewater genomic surveillance has proved to be an valuable tool in the public health world!

CDC leaders attempt to reassure staff after shooting, but meeting is brief An all-hands meeting at the CDC to discuss the attack on the agency on Friday was brief and chaotic, staffers say.

Rocky start for new #CDC director Susan Monarez, whose first week was punctuated by Friday's attack. Her first all-hands meeting lasted ~13 minutes, with technical challenges with dead air for a time & some staff unable to join the call. "This is a mess," one said. www.statnews.com/2025/08/12/c...

Real-time, multi-pathogen wastewater genomic surveillance with Freyja 2 Case-based infectious disease surveillance is fundamental to public health, but is resource-intensive, logistically complex, and prone to sampling bias. Wastewater testing and sequencing have increasi...

@kevinlibuit.bsky.social & @curtiskapsak.bsky.social were two of the co-authors on a new paper on Freyja 2 — a bioinformatics tool for real-time, multi-pathogen wastewater surveillance.

Read about it here: www.medrxiv.org/content/10.1...

Real-time, multi-pathogen wastewater genomic surveillance with Freyja 2 Case-based infectious disease surveillance is fundamental to public health, but is resource-intensive, logistically complex, and prone to sampling bias. Wastewater testing and sequencing have increasi...

A few days ago we preprinted our Freyja 2 paper, describing the expansion of our original Freyja method to a real-time, multi-pathogen surveillance tool to track pathogen lineage prevalence and dynamics from sequencing of wastewater and other complex samples (like milk). 🧵
 doi.org/10.1101/2025...

Pleased to say that our preprint benchmarking Nanopore data for MLST, cgMLST, cgSNP & AMR typing from bacterial isolates is out! TL;DR you can get almost perfect results from 50x depth using live SUP basecalling with a GPU in under 20 hours #microsky#IDsky 🦠🧬🖥️ /1
www.medrxiv.org/content/10.1...

Congrats to you and the team that put this all together. So excited to dive deeper and utilize those datasets. Thank you all so much!!

Schrier to RFK Jr: You gave Cassidy the answer he needed to hear in order to get his confirmation vote, then as soon as you were secretary you turned around & fired all 17 members. You lied. I also want to be clear that I will lay all responsibility for every vaccine-preventable death at your feet.

RUIZ: Did you read the report & fact-check its sources prior to publication?

RFK JR: I did not fact check

RUIZ: It included citations to sources that don't exist. How does that happen?

RFK JR: All of the foundational assertions are accurate

RUIZ: They did not exist. How can they be accurate?

Advantages of Software Containerization in Public Health Infectious Disease Genomic Surveillance wwwnc.cdc.gov/eid/article/... 🧬🖥️🧪

You might be wondering why we haven't updated outbreak.info for months.

Well, the reason is that GISAID cut our access in January - as they did others. Without telling us.

After a ♾️ back and forth, that is now permanent.

More on that soon - and why GISAID should not be trusted with critical data.