# Welcome to Pathogenwatch

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[A "Getting Started" Tutorial](/old.pathogenwatch/a-getting-started-tutorial.md)
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For latest news and notices of upcoming maintenance or other PW related events visit the [Announcements](/old.pathogenwatch/announcements.md) page.
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## 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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# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://cgps.gitbook.io/old.pathogenwatch/readme.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.