Pathoplexus

@pathoplexus.org

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

A photo of Placide Mbala
A gif showing someone searching in the free-text field in the 'Docs' section - searching 'SeqSets' and exploring pages related to the results.
Screenshot of our rich XLSX template showing dropdowns for fields with defined values - this one shows a list of Countries
Gif of a sequence page on Pathoplexus with multiple version. The user clicks on the 'Version' dropdown in the top-right and selects 'compare versions' - which then highlights the fields that have changed between versions.
A gif showing the search page for Dengue virus, with someone slowly typing in 'mosquitos' and having the box find all mosquito species, then finally showing the 'Culicidae' entry to cover all mosquitos when the final 's' is typed.
Screenshot of a SeqSet page, showing that the SeqSet has been cited in a paper, with a link to that paper.
Screenshot of the Pathoplexus website homepage
Screenshot of the first page of the pathoplexus annual report 2024-2025, which includes the first few lines of the report, describing the founding of Pathoplexus in August 2024
A screenshot of all supported viruses on the Pathoplexus front page, with ANDV and BDBV highlighted.
Image of some of the available pathogens on Pathoplexus, with a red rectangle outlining the new tile for Ebola Bundibugyo virus, with 44 sequences.
Screenshot showing that if you try to have a group name that already exists, Pathoplexus will now warn you to create a more unique name.
Screenshot of the Pathoplexus website, showing the 'browse data' page for CCHF - highlighting how you can now add mutations in specific boxes for the S, M, & L segments, rather than having to append the segment to the mutation itself.
picture of Dr Idrissa Dieng, smiling, in a green outfit
A screenshot of the new Pathoplexus homepage showing all viruses now supported, including Dengue and Yellow Fever, which are circled in red
A screenshot of the front page of Pathoplexus' website, showing the addition of a tile for Marburg Virus.
Photographs of the PHA4GE pre-conference workshops. Showing first a photo of the workshop organizers, Patricia, Emma, Arthur, Stephen, and Chaoran. Then a photo of Stephen helping a workshop participant, and a photo of Chaoran helping a workshop participant.
A screenshot of the Tools page in RSV-A on Pathoplexus, highlighting GenSpectrum, Nextstrain, and some simple plots
Screenshot showing the search panel in Pathoplexus, showing that one can now select, for example, two Submitting Groups and two Countries in your sequence search
Graph showing the change in number of directly submitted sequences to Pathoplexus since August 2024. 0 in Aug 2024 to almost 9000 today.
Screenshot of the Pathoplexus Data Use Terms, focusing on 4.2, Restricted Use Data introduction
Screenshot of the search page on Pathoplexus showing the first 4 sequences: their Pathoplexus accession, sample date, collection country and subdivision, authors, affiliations, and length.
Screenshot of list of authors, which can be seen in the post link in the first tweet
An abstract image showing a world map made of small, colorful lines, as featured on ETH4D website, overlayed with the ETH4D logo itself.
A gif showing how the new accession search works on the Pathoplexus homepage - clicking on the magnifying glass icon in the top menu expands it, and you can type or paste in an accession to go straight there.
A screenshot of the Pathoplexus homepage, now showing Measles among the other pathogens supported.
A photo of key members of the Pathoplexus developer team receiving the ORD prize
A diagram showing a timeline from August 2024 to May 2025, with one stop in the middle at December 2024. In August, four viruses are shown: Ebola Sudan & Zaire, West Nile, and CCHF. In December 2024, mpox is added. Then in May 2025, RSV & HMPV
An image of a birthday cake with scientific doodles around it, 9 colourful candles, and the Pathoplexus logo in the middle, with the words 'Happy 1 year'
Graph showing 6 months of Mpox sequences added to Pathoplexus, from Feb 2025 - July 2025, as a bar-chart. Bars are split into blue (sequences ingested from NCBI) and orange (sequences uploaded directly to Pathoplexus). The totals are approximately: - Feb: 75 from NCBI, 725 direct - Mar: 50 NCBI, ~5 direct - Apr: 75 NCBI, 225 direct - May: 100 NCBI, 100 direct - June: 50 NCBI, 75 direct - July: too small to see clearly
Screenshot of the July Update News article on the Pathoplexus website
A diagram showing how users can easily upload data to Pathoplexus and choose to share this as 'Open data' which can be used by other without restriction, or 'Restricted-use' data which requires permission to publish or preprint on. Restricted-use data can be restricted for up to 1 year, after which it becomes Open, and is always available to view. Open data is automatically submitted to INDSC (Genbank, ENA, DDBJ) by Pathoplexus on behalf of the submitter.
Screenshot of the homepage of Pathoplexus, showing tiles to navigate to the supported pathogens CCHF, Ebola Sudan, Ebola Zaire, HMPV, Mpox, RSV-A, RSV-B, and West Nile virus.
A video showing how when you add filters on a Pathoplexus sequence search page, those filters appear at the top of the page, showing which ones are currently applied. Filters can also be removed by deleting them there.
A screenshot of the pathoplexus website, showing a form where you can upload a single sequence by filling in the fields.
A video showing how users can select which field their metadata file columns should be mapped to, even if their column names do not match the Pathoplexus column names.
Screenshot of the virological post on the Ebolavirus sequence