**Pathogenwatch** is a user-friendly web platform empowering researchers and public health professionals to analyse and visualise genomic data from microbial pathogens.
**Designed** to streamline pathogen surveillance, it integrates advanced tools for resistance gene detection, lineage identification, and outbreak tracking, with interactive visualisations and access to global databases.
**Cutting-edge** genomic analysis combined with seamless data sharing, Pathogenwatch enables faster, more informed decision-making to combat antimicrobial resistance and monitor the spread of infectious diseases worldwide.
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**To get started,** [**sign in**](https://next-docs.pathogen.watch/getting-started/sign-in) **and then take a "**[**Brief Tour of Pathogenwatch**](https://next-docs.pathogen.watch/getting-started/a-brief-tour-of-pathogenwatch)**". Learn even more in the "How to use Pathogenwatch" pages.**
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{% tabs %}
{% tab title="Upload" %}
#### Upload microbial genomes to initiate a suite of automated analyses
* Tools include:
* Species assignment using "[Speciator](https://next-docs.pathogen.watch/technical-descriptions-of-analysis-tools/speciator)".
* Over 20 [core genome MLST](https://next-docs.pathogen.watch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/cgmlst) schemes.
* Typing with classic [MLST](https://next-docs.pathogen.watch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/mlst), [Genotyphi](https://next-docs.pathogen.watch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/genotyphi), [NG-MAST](https://next-docs.pathogen.watch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/ng-mast), PopPUNK and others.
* [Antibiotic resistance](https://next-docs.pathogen.watch/technical-descriptions-of-analysis-tools/antimicrobial-resistance-prediction) prediction.
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Your submitted genome data is kept private unless you select sharing.
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{% content-ref url="how-to-use-pathogenwatch/uploads-and-folders/genome-uploads-folders" %}
[genome-uploads-folders](https://next-docs.pathogen.watch/how-to-use-pathogenwatch/uploads-and-folders/genome-uploads-folders)
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{% tab title="Browse" %}
#### Browse published [genomes](https://next.pathogen.watch/genomes) and [collections](https://next.pathogen.watch/collections) direct from the CGPS
* Daily updates of assemblies for core species, including [WHO priority pathogens](https://next-docs.pathogen.watch/old-who-bacterial-priority-pathogens), from the [SRA](https://www.ncbi.nlm.nih.gov/sra) via our real time assembly pipeline.
* We provide extensive collections of publicly available microbial sequences, gathered by publication or survey where possible.
{% content-ref url="how-to-use-pathogenwatch/browsing-and-viewing-genomes/browsing-searching-genomes" %}
[browsing-searching-genomes](https://next-docs.pathogen.watch/how-to-use-pathogenwatch/browsing-and-viewing-genomes/browsing-searching-genomes)
{% endcontent-ref %}
{% content-ref url="how-to-use-pathogenwatch/collections/browsing-collections" %}
[browsing-collections](https://next-docs.pathogen.watch/how-to-use-pathogenwatch/collections/browsing-collections)
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{% tab title="Search" %}
#### Search the genomic neighbourhood using cgMLST
* We have incorporated over 20 cgMLST schemes from multiple sources, including [PubMLST](https://pubmlst.org/) and the [Pasteur Institute](https://bigsdb.pasteur.fr/).
* A clustering-based system allows the identification of near neighbours to give your uploads a context.
{% content-ref url="technical-descriptions-of-analysis-tools/trees-clustering-and-context-search/cgmlst-clustering" %}
[cgmlst-clustering](https://next-docs.pathogen.watch/technical-descriptions-of-analysis-tools/trees-clustering-and-context-search/cgmlst-clustering)
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{% tab title="Investigate" %}
#### Create & interact with collections for a deeper view
* Create a single collection integrating public genomes with your own.
* Make the collection public to share your insights with other researchers.
* The powerful [Interactive Collection View](https://next-docs.pathogen.watch/how-to-use-pathogenwatch/collections/using-the-icv) integrates the CGPS [Phylocanvas](http://phylocanvas.org/) tree panel with a map panel and data tables, along with a query tool for highlighting genomes with particular features.
{% content-ref url="how-to-use-pathogenwatch/collections/creating-sharing-collections" %}
[creating-sharing-collections](https://next-docs.pathogen.watch/how-to-use-pathogenwatch/collections/creating-sharing-collections)
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{% content-ref url="how-to-use-pathogenwatch/collections/using-the-icv" %}
[using-the-icv](https://next-docs.pathogen.watch/how-to-use-pathogenwatch/collections/using-the-icv)
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{% endtab %}
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For latest news and notices of upcoming maintenance or other PW related events visit the [**Announcements**](https://next-docs.pathogen.watch/news-and-release-notes/announcements) page.
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***
Pathogenwatch is provided by the Centre for Genomic Pathogen Surveillance
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