We develop open web APIs and dashboards for genomic epidemiology. Monkeypox - mpox.genspectrum.org and SARS-CoV-2 - cov-spectrum.org
Joined October 2021
- Tweets 169
- Following 21
- Followers 1,356
- Likes 58
60 Photos and videos
28 Aug 2025
Finally, CoV-Spectrum is meeting trees 🌳 – this week, we released a new feature to browse the SARS-CoV-2 UShER tree on CoV-Spectrum. With the new feature, you can see a subtree of your variant of interest. 1/4
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28 Aug 2025
The feature is only available on open.cov-spectrum.org/ which uses data from INSDC (GenBank/ENA/DDBJ), we unfortunately cannot provide it for data from GISAID.
If you have any questions or suggestions, please let us know! 3/4
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28 Aug 2025
Thank you very much to the UShER team (Jakob McBroome, @AngieSHinrichs, @RussCorbett, @yatishturakhia, and many more) for providing the daily-updated trees, @theosanderson for developing Taxonium (and adding several features upon request!) and @CDC_AMD for funding. 4/4
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14 Jan 2025
We have just received an updated dataset from GISAID. Many thanks to the GISAID team for fixing the data feed!
10 Jan 2025
Information for CoV-Spectrum users: The GISAID data on CoV-Spectrum has not been updated since 23 December due to an interruption in the data feed. We have contacted GISAID regarding this issue and are hopeful for a resolution soon.
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10 Jan 2025
Information for CoV-Spectrum users: The GISAID data on CoV-Spectrum has not been updated since 23 December due to an interruption in the data feed. We have contacted GISAID regarding this issue and are hopeful for a resolution soon.
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16 Dec 2024
GenSpectrum just added a mpox dashboard using data from @Pathoplexus – see genspectrum.org
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25 Nov 2024
Our new GenSpectrum.org dashboard has finally launched! Using Influenza H5N1, RSV and SARS-CoV-2 data from INSDC and West Nile virus data from @pathoplexus, it enables fast and interactive analyses of genome sequencing data similar to CoV-Spectrum. 1/5
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25 Nov 2024
Our tool is of course fully open source. Please let us know if you have any feedback or a suggestion for what should be added or improved. You can create an issue in our GitHub repository: github.com/GenSpectrum/dashb… 4/5
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25 Nov 2024
We would like to thank all the data generators for making their data openly available, @ETH_en, the US @CDCgov and the Office of Advanced Molecular Detection (@CDC_AMD) for funding and the whole team (github.com/GenSpectrum#contr…) for the amazing work! 5/5
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GenSpectrum retweeted
27 Aug 2024
It was an amazing journey for us (our research team @ETH_en with the support of contracted software developers from TNG technology) to work with colleagues across the globe from the first idea to what we now call Pathoplexus pathoplexus.org! We are very proud to 1/2
27 Aug 2024
📢 We're excited to introduce Pathoplexus, a specialized sequence database for human viral pathogens! 🌍 🧬
Launching with 4 viruses, Pathoplexus.org combines modern open-source software with transparent governance to improve global pathogen sequence sharing.
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GenSpectrum retweeted
27 Aug 2024
💡 Want to learn more or get involved? Visit Pathoplexus.org, follow us here, or join the discussion on our forums (discussion.pathoplexus.org/)!
Together, we can create a more equitable & collaborative environment for global pathogen research! 🎉 #Pathoplexus
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GenSpectrum retweeted
27 Aug 2024
📢 We're excited to introduce Pathoplexus, a specialized sequence database for human viral pathogens! 🌍 🧬
Launching with 4 viruses, Pathoplexus.org combines modern open-source software with transparent governance to improve global pathogen sequence sharing.
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25 Oct 2023
Interested in developing dashboards and tools for public health and genomic epidemiology? We are looking for a software engineer to join our GenSpectrum team at @ETH_BSSE in Basel, 🇨🇭CH!
jobs.ethz.ch/job/view/JOPG_e…
Please reach out if you have any questions and please share! :)
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19 Aug 2023
CoV-Spectrum now uses the most recent Nextclade dataset and calls BA.2.86. cov-spectrum.org/explore/Wor…
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GenSpectrum retweeted
24 May 2023
You can now use a chatbot to find out latest information about SARS-CoV-2 variants arxiv.org/abs/2305.13821 cov-spectrum.org/chat @GenSpectrum in your favorite language, including Swiss German! The chat relies on the millions of available SARS-CoV-2 sequences, answering 1/2
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GenSpectrum retweeted
19 Apr 2023
Do you want to find out details about the circulating SARS-CoV-2 variants? Then chat to cov-spectrum.org/chat - it can provide answers to questions for which even the cov-spectrum.org dashboard has no direct information. We would be grateful if you allow the 1/2
19 Apr 2023
💬 You can now chat with CoV-Spectrum! 💬
Backed by @OpenAI #ChatGPT (GPT-3.5), it’s now possible to ask questions about variants in a chat style at cov-spectrum.org/chat. It can even answer questions that the dashboard can’t! 🚀 Here are some examples. 1/
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GenSpectrum retweeted
19 Apr 2023
Here it is variant chatbot! This is likely among the best possible uses for AI to manage big data at the time of a pandemic ! @EricTopol @DrEricDing @TRyanGregory @RobiVil @PeacockFlu
19 Apr 2023
💬 You can now chat with CoV-Spectrum! 💬
Backed by @OpenAI #ChatGPT (GPT-3.5), it’s now possible to ask questions about variants in a chat style at cov-spectrum.org/chat. It can even answer questions that the dashboard can’t! 🚀 Here are some examples. 1/
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