Welcome to Pathogenwatch

Overview and Key Links.
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Upload microbial genomes to access an array of automatic analyses

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.

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.

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)[] 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.
Last modified 11mo ago