Welcome to Pathogenwatch

Overview and Key Links.

▶️A "Getting Started" Tutorial

Upload microbial genomes to access an array of automatic analyses

Uploading Genomes

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.

Browsing GenomesBrowsing Collections

Search the genomic neighbourhood using cgMLST

  • We have incorporated over 20 cgMLST schemes from multiple sources, including PubMLST and the Pasteur Institute.

  • A clustering-based system allows the identification of near genomic neighbours to give your uploads a context.

cgMLST Clustering

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.

Creating A CollectionUsing The Interactive Collection Views

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