Welcome to Pathogenwatch

Overview and Key Links.

▶️A "Getting Started" Tutorial

For latest news and notices of upcoming maintenance or other PW related events visit the Announcements page.

Upload microbial genomes to access an array of automatic analyses

• Species assignment using "Speciator".

• Over 20 core genome MLST schemes.

• Typing with classic MLST, Genotyphi, NG-MAST, PopPUNK and others.

• Antibiotic resistance prediction.

• Interrogate the database using cgMLST-based clustering and SNP trees.

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 Collection

Using The Interactive Collection Views