Pathoplexus@pathoplexus

An open-source pathogen sequence database dedicated to equitable sharing, transparent governance, & empowering global public health.

pathoplexus.org
Joined March 2024
67 Photos and videos
1/ 🧬 A big #Pathoplexus milestone: you can now optionally include raw sequencing reads alongside your consensus sequences! Hosting raw reads alongside consensus data helps improve reproducibility & allow in-depth analyses. 📰 Read more: pathoplexus.org/news/2026-09…
AI-generated image showing raw reads (short reads) lining up above a consensus sequence, with both the raw reads and consensus sequence labelled. Vague images below show a virus, coverage, and DNA.

ALT AI-generated image showing raw reads (short reads) lining up above a consensus sequence, with both the raw reads and consensus sequence labelled. Vague images below show a virus, coverage, and DNA.

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2/ ⚙️ How it works: raw reads follow all the same policies as consensus sequences - your chosen Data Use Terms apply to both, and raw reads are openly downloadable as soon as processing completes. Pathoplexus handles INSDC submission for you, just like today.
Screenshot of the submission page showing the section to upload raw-reads - with a description and link to the documentation on the left, and a place to upload folders and files on the right.

ALT Screenshot of the submission page showing the section to upload raw-reads - with a description and link to the documentation on the left, and a place to upload folders and files on the right.

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3/ 📤 Ready to try it? Upload raw reads files alongside your next submission (individual or bulk), add them to your existing consensus sequences, and check out our docs for the details on required metadata. 🔗 pathoplexus.org/news/2026-09… #OpenData #OpenScience #PathogenGenomics

Pathoplexus | Pathoplexus announces support for raw reads

Pathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.

pathoplexus.org
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1/ 🎂 Pathoplexus turns TWO! 🎉 Two years ago we launched with an idea: what if pathogen data sharing put open access, speed, ease of use, & credit for data generators at its center? Here's what our community has built since: 📰 Read the full update: pathoplexus.org/news/2026-08…
AI generated watercolor-style image of a white birthday cake with blue and gold small decorate balls around the base and top, with a blue Pathoplexus logo on the side. On top, is a gold and white '2' candle that's lit. From the cake come strands of blue and gold, representing stylized DNA, network nodes, and ribbons representing credit and attribution.

ALT AI generated watercolor-style image of a white birthday cake with blue and gold small decorate balls around the base and top, with a blue Pathoplexus logo on the side. On top, is a gold and white '2' candle that's lit. From the cake come strands of blue and gold, representing stylized DNA, network nodes, and ribbons representing credit and attribution.

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8/ 🙏 None of this happens on its own. Thank you to our Executive Board, our members who guide and hold us accountable, our developer team, and every researcher, lab, and institute who has chosen to share data through Pathoplexus.
Grid of photographs of all 32 members of Pathoplexus

ALT Grid of photographs of all 32 members of Pathoplexus

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9/ ❤️ To everyone who's submitted a sequence, flagged a curation issue, joined our Scientific Advisory Board, presented a poster, funded our work, or told a colleague about us - thank you. 2️⃣ Here's to year two, and many more to come! 🎊 🔗 Full post: pathoplexus.org/news/2026-08…

Pathoplexus | Pathoplexus Turns Two

Pathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.

pathoplexus.org
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1/ 🦟 New on @Pathoplexus: Zika virus (ZIKV) is now supported! Share your ZIKV sequences as Open or Restricted-Use, just like our other pathogens. Read more: pathoplexus.org/news/2026-08… 📰
Screenshot of the Pathoplexus website homepage, where the new Zika virus button is circled in red

ALT Screenshot of the Pathoplexus website homepage, where the new Zika virus button is circled in red

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2/ 🧬 ZIKV often causes mild or no symptoms - but can rarely lead to Guillain-Barré syndrome or birth defects, making surveillance important. 🙏 Thanks to @ArthurShem for leading this addition, & as always, to our submitters, curators, & community for helping expand Pathoplexus!
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1/ Using @pathoplexus sequences in a preprint or publication? Remember to cite them correctly! It's easy - here how! 1. 🧺Create a SeqSet containing all the sequences used. You can divide them into Focal & Background pathoplexus.org/docs/how-to/…
Screenshot of the 'Create a SeqSet' page on Pathoplexus, showing where one can fill in the SeqSet name, description, and the sequences used, divided into Focal and Background

ALT Screenshot of the 'Create a SeqSet' page on Pathoplexus, showing where one can fill in the SeqSet name, description, and the sequences used, divided into Focal and Background

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3/ 3. ✒️Cite the DOI *in the references*, like a paper! (This is how CrossRef 'sees' it & how we track it) Getting a citation is easy - click the 'Export/Cite' button & pick your style Copy this *into the references* just like you'd cite a paper!
Screenshot of the SeqSet Details page on Pathoplexus, showing the name, description, and other metrics - now also showing a DOI in place of the previous link to generate a DOI. Highlighted is the location of the button showing 'Export/Cite' which allows generation of citation/reference text.

ALT Screenshot of the SeqSet Details page on Pathoplexus, showing the name, description, and other metrics - now also showing a DOI in place of the previous link to generate a DOI. Highlighted is the location of the button showing 'Export/Cite' which allows generation of citation/reference text.

Screenshot of the SeqSet 'Export/Cite SeqSet' popup on Pathoplexus, which appears after pressing the previous button. The popup allows download of the data as JSON or TSV, and below that, a text box that allows the user to easily copy citation/reference text for the SeqSet in BibTeX, MLA, or APA style. This includes the name of the SeqSet, year, and DOI.

ALT Screenshot of the SeqSet 'Export/Cite SeqSet' popup on Pathoplexus, which appears after pressing the previous button. The popup allows download of the data as JSON or TSV, and below that, a text box that allows the user to easily copy citation/reference text for the SeqSet in BibTeX, MLA, or APA style. This includes the name of the SeqSet, year, and DOI.

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4/ That's it! 🎉 Now, as soon as CrossRef indexes your manuscript, your SeqSet, and all sequences within that SeqSet, will show that paper/preprint! See examples - A preprint citation in a SeqSet: pathoplexus.org/seqsets/PP_S… A preprint on a sequence page: pathoplexus.org/seq/PP_000TC…
Screenshot of a different SeqSet Details page on Pathoplexus - this SeqSet has been used and cited. It shows the name, description, and other metrics, but importantly, below the DOI, shows a list of citations. This SeqSet shows it's been cited in a paper called 'Improving the Scalability of Bayesian Phylodynamic Inference through Efficient MCMC Proposals'

ALT Screenshot of a different SeqSet Details page on Pathoplexus - this SeqSet has been used and cited. It shows the name, description, and other metrics, but importantly, below the DOI, shows a list of citations. This SeqSet shows it's been cited in a paper called 'Improving the Scalability of Bayesian Phylodynamic Inference through Efficient MCMC Proposals'

Screenshot a Pathoplexus Sequence Details page, of a sequence that is within the SeqSet shown previously. This shows the sequence name, sample date, and other sequence metrics, but since it is included in a SeqSet that has been cited, it also shows a 'Cited by' section, which lists all citations. It shows it has been cited by the same paper in the SeqSet, 'Improving the Scalability of Bayesian Phylodynamic Inference through Efficient MCMC Proposals'

ALT Screenshot a Pathoplexus Sequence Details page, of a sequence that is within the SeqSet shown previously. This shows the sequence name, sample date, and other sequence metrics, but since it is included in a SeqSet that has been cited, it also shows a 'Cited by' section, which lists all citations. It shows it has been cited by the same paper in the SeqSet, 'Improving the Scalability of Bayesian Phylodynamic Inference through Efficient MCMC Proposals'
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1/ 🛠️ Our July update is here - and it's a technical one! New features for citations, search, submission, and more. Here's what's new in #Pathoplexus 👇 🔗 Full post: pathoplexus.org/news/2026-07…
Screenshot of the Pathoplexus website homepage

ALT Screenshot of the Pathoplexus website homepage

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9/ 🏛️ Governance update: Pathoplexus held its General Assembly on 10 June, approving the annual report & planning next year. Minutes & report here 👉 pathoplexus.org/about/govern… We're also delighted to welcome Prof. Placide Mbala @PlacideMbala to our Scientific Advisory Board! 🎉
A photo of Placide Mbala

ALT A photo of Placide Mbala

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10/ As always - share sequences, cite your SeqSets & DOIs, and let us know what you'd like to see next 💬 🔗 Full July update: pathoplexus.org/news/2026-07… #OpenData #OpenScience #PathogenGenomics #PublicHealth

Pathoplexus | Pathoplexus July Update

Pathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.

pathoplexus.org
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