# Welcome to Pathogenwatch

<div data-full-width="true"><figure><img src="https://3802074513-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FHXfIP1DQQRf1INOFCCsK%2Fuploads%2F4vzx1Wty44KLOijN3kjI%2Fpw-logo-full-rgb.png?alt=media&#x26;token=6246f730-1225-419a-b7cc-11f9293dff99" alt="" width="461"><figcaption></figcaption></figure></div>

**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.

{% hint style="success" %}
**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.**
{% endhint %}

{% 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.

{% hint style="info" %}
Your submitted genome data is kept private unless you select sharing.
{% endhint %}

{% 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)
{% endcontent-ref %}
{% endtab %}

{% 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)
{% endcontent-ref %}
{% 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="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)
{% endcontent-ref %}
{% endtab %}

{% 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)
{% endcontent-ref %}

{% 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)
{% endcontent-ref %}
{% endtab %}
{% endtabs %}

{% hint style="info" %}
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.
{% endhint %}

***

<figure><img src="https://3802074513-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FHXfIP1DQQRf1INOFCCsK%2Fuploads%2FNh7mexAAgYjWSK2Qb1zv%2Fcgps-logo-full-rgb.png?alt=media&#x26;token=f6f86989-d984-40bd-8010-ddc83d9c59f0" alt="Centre for Genomic Pathogen Surveillance"><figcaption><p>Pathogenwatch is provided by the Centre for Genomic Pathogen Surveillance</p></figcaption></figure>