Welcome to Pathogenwatch
Overview and Key Links.
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Upload microbial genomes to access an array of automatic analyses
Species assignment using "Speciator".
Over 20 core genome MLST schemes.
Antibiotic resistance prediction.
Interrogate the database using cgMLST-based clustering and SNP trees.
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)[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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