Nextstrain is happy to announce a major update to our tuberculosis analysis, making it our first real-time (continually updated) analysis for a bacterial pathogen. Please see our new blog post for details:
nextstrain.org/blog/2025-11...
Full blog post explaining situation and background is available here:
nextstrain.org/blog/2025-11...
Closing these public analyses puts the world more in the dark and concretely harms surveillance as it becomes more difficult for variant spotters to contribute to global situational awareness. 4/5
Tools like Nextstrain, CoV-Spectrum, UShER and outbreak.info facilitate a global community of experts to keep close tabs on the ongoing evolution of SARS-CoV-2. Support for outbreak.info ended in Jan 2025 and CoV-Spectrum hasn't been updated for >3 weeks. 3/5
We strive to credit labs collecting specimens and generating sequence data prominently. But credit for data contributions is not zero sum – surfacing of data in popular tools generates visibility and does not infringe on future publications by the data generators. 2/5
On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
Nextstrain is happy to announce the availability of new resources for mumps, as described in our recent blog post. We welcome any feedback on these new resources!
nextstrain.org/blog/2025-09...
Nextstrain is happy to announce the availability of a Rubella dataset — please see our new blog post for details. We welcome feedback from Rubella researchers on these new resources!
The Nextstrain team has updated our core pathogen workflows to be compatible with Snakemake v8 or higher and has updated the Nextstrain runtimes to include Snakemake v9. Please see our new blog post for more details:
Happy Friday! We've got a new blog post all about a new feature that was recently added to the Nextstrain CLI: `nextstrain run`
This is a foundational component for a new, easier way to re-use Nextstrain workflows, take a look!
nextstrain.org/blog/2025-06...
Fantastic training by @aphl.org and @unmc.bsky.social (Dr. Shaun Cross) with Uganda CPHL on @nextstrain.org data viz for #mpox & #Ebola Sudan virus. The workshop brought together lab, epi, and IT staff—and by the end, they were building phylogenetic trees for other pathogens too! 🧬🌍 #GenomicEpi
We are happy to announce a new blog post at nextstrain.org, highlighting some recently-added resources for rabies, Lassa fever, and yellow fever virus:
nextstrain.org/blog/2025-02...
We'd love to hear feedback from any subject matter experts with experience with any of those viruses!
Hi -- if you contact us at hello@nextstrain.org, we can try to assist.
