> For the complete documentation index, see [llms.txt](https://cgps.gitbook.io/pathogenwatch/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cgps.gitbook.io/pathogenwatch/readme.md).

# Welcome to Pathogenwatch

**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**](/pathogenwatch/getting-started/sign-in.md)  **and then take a "**[**Brief Tour of Pathogenwatch**](/pathogenwatch/getting-started/a-brief-tour-of-pathogenwatch.md)**". Learn even more in the "How to use Pathogenwatch" pages.**
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#### Upload microbial genomes to initiate a suite of automated analyses

* Tools include:
  * Species assignment using "[Speciator](/pathogenwatch/technical-descriptions-of-analysis-tools/speciator.md)".
  * Over 20 [core genome MLST](/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/cgmlst.md) schemes.
  * Typing with classic [MLST](/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/mlst.md), [Genotyphi](/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/genotyphi.md), [NG-MAST](/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/ng-mast.md), PopPUNK and others.
  * [Antibiotic resistance](/pathogenwatch/technical-descriptions-of-analysis-tools/antimicrobial-resistance-prediction.md) prediction.

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Your submitted genome data is kept private unless you select sharing.
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{% content-ref url="/pages/baTSMfFMSY3Pg4PIexkB" %}
[Genome Uploads & Projects](/pathogenwatch/how-to-use-pathogenwatch/uploads-and-folders/genome-uploads-folders.md)
{% endcontent-ref %}
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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](/pathogenwatch/old-who-bacterial-priority-pathogens.md), 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="/pages/P8b4ztIUw72rv41RXihc" %}
[Browsing & Searching Genomes](/pathogenwatch/how-to-use-pathogenwatch/browsing-and-viewing-genomes/browsing-searching-genomes.md)
{% endcontent-ref %}

{% content-ref url="/pages/rWtbtk3wdF8RZYKMDBws" %}
[Browsing Collections](/pathogenwatch/how-to-use-pathogenwatch/collections/browsing-collections.md)
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{% endtab %}

{% 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="/pages/lpscPDMm6hovWcESOgfg" %}
[cgMLST Clustering & Context Searching](/pathogenwatch/technical-descriptions-of-analysis-tools/trees-clustering-and-context-search/cgmlst-clustering.md)
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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](/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv.md) 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="/pages/hG0OpfQ46NizKFQ6M9ES" %}
[Creating & Sharing Collections](/pathogenwatch/how-to-use-pathogenwatch/collections/creating-sharing-collections.md)
{% endcontent-ref %}

{% content-ref url="/pages/ylSCofXClj3CSFkDEVPH" %}
[Using The Interactive Collection View](/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv.md)
{% endcontent-ref %}
{% endtab %}
{% endtabs %}

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For latest news and notices of upcoming maintenance or other PW related events visit the [**Announcements**](/pathogenwatch/news-and-release-notes/announcements.md) page.
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***

<div align="center"><figure><img src="/files/XKXyWBqfsY3zGsntVBoI" alt="Centre for Genomic Pathogen Surveillance" width="563"><figcaption><p>Pathogenwatch is provided by the Centre for Genomic Pathogen Surveillance</p></figcaption></figure></div>