# Welcome to Pathogenwatch

<img src="https://321039241-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LB6jV5PGtOeTCAE8S8I%2F-LBQfhByzSZIKSEK9n46%2F-LBQfrhXDJ6u8qvyjrbY%2Fpwatch_full_logo.svg?alt=media&#x26;token=d5933f01-cccc-4225-8644-223aabab79fe" alt="" data-size="original">

{% content-ref url="a-getting-started-tutorial" %}
[a-getting-started-tutorial](https://cgps.gitbook.io/pathogenwatch/a-getting-started-tutorial)
{% endcontent-ref %}

{% hint style="danger" %}
For latest news and notices of upcoming maintenance or other PW related events visit the [Announcements](https://cgps.gitbook.io/pathogenwatch/announcements) page.
{% endhint %}

## Upload microbial genomes to access an array of automatic analyses

* Species assignment using "[Speciator](https://cgps.gitbook.io/pathogenwatch/technical-descriptions/species-assignment)".
* Over 20 [core genome MLST](https://cgps.gitbook.io/pathogenwatch/technical-descriptions/typing-methods/cgmlst) schemes.
* Typing with classic [MLST](https://cgps.gitbook.io/pathogenwatch/technical-descriptions/typing-methods/mlst), [Genotyphi](https://cgps.gitbook.io/pathogenwatch/technical-descriptions/typing-methods/genotyphi), [NG-MAST](https://cgps.gitbook.io/pathogenwatch/technical-descriptions/typing-methods/ng-mast), PopPUNK and others.
* [Antibiotic resistance](https://cgps.gitbook.io/pathogenwatch/technical-descriptions/antimicrobial-resistance-prediction/pw-amr) prediction.
* Interrogate the database using [cgMLST-based clustering](https://cgps.gitbook.io/pathogenwatch/technical-descriptions/cgmlst-clusters) and [SNP trees](https://cgps.gitbook.io/pathogenwatch/technical-descriptions/core-genome-tree).

{% content-ref url="how-to-use-pathogenwatch/uploading-assemblies" %}
[uploading-assemblies](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/uploading-assemblies)
{% endcontent-ref %}

## Browse published collections and sequences direct from the CGPS

* We provide extensive collections of publicly available microbial sequences, gathered by publication or survey where possible.
* Imported genomes are automatically annotated with our in-house pipelines and the results available for download.

{% content-ref url="how-to-use-pathogenwatch/browsing-genomes" %}
[browsing-genomes](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/browsing-genomes)
{% endcontent-ref %}

{% content-ref url="how-to-use-pathogenwatch/browsing-collections" %}
[browsing-collections](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/browsing-collections)
{% endcontent-ref %}

## 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 genomic neighbours to give your uploads a context.

{% content-ref url="technical-descriptions/cgmlst-clusters" %}
[cgmlst-clusters](https://cgps.gitbook.io/pathogenwatch/technical-descriptions/cgmlst-clusters)
{% endcontent-ref %}

## Create collections for a deeper view

* Use the powerful selection tool to integrate public genomes with your own and create a single collection.
* The collection view integrates the CGPS (Phylocanvas)\[<http://phylocanvas.org/>] tree browser with an interactive map display and metadata tables, along with a query tool for highlighting genomes with particular features.
* Make the collection public and share your insights with other researchers.

{% content-ref url="how-to-use-pathogenwatch/creating-a-collection" %}
[creating-a-collection](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/creating-a-collection)
{% endcontent-ref %}

{% content-ref url="how-to-use-pathogenwatch/collection-view" %}
[collection-view](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collection-view)
{% endcontent-ref %}