> For the complete documentation index, see [llms.txt](https://cgps.gitbook.io/old.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/old.pathogenwatch/readme.md).

# Welcome to Pathogenwatch

<img src="/files/-LBQfrhXDJ6u8qvyjrbY" alt="" data-size="original">

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[A "Getting Started" Tutorial](/old.pathogenwatch/a-getting-started-tutorial.md)
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{% hint style="danger" %}
For latest news and notices of upcoming maintenance or other PW related events visit the [Announcements](/old.pathogenwatch/announcements.md) page.
{% endhint %}

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

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

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[Uploading Genomes](/old.pathogenwatch/how-to-use-pathogenwatch/uploading-assemblies.md)
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## 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.

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[Browsing Genomes](/old.pathogenwatch/how-to-use-pathogenwatch/browsing-genomes.md)
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[Browsing Collections](/old.pathogenwatch/how-to-use-pathogenwatch/browsing-collections.md)
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## 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.

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[cgMLST Clustering](/old.pathogenwatch/technical-descriptions/cgmlst-clusters.md)
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## 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.

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[Creating A Collection](/old.pathogenwatch/how-to-use-pathogenwatch/creating-a-collection.md)
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[Using The Interactive Collection Views](/old.pathogenwatch/how-to-use-pathogenwatch/collection-view.md)
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