Welcome to Pathogenwatch

Overview and Key Links.

▶️pageA "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.

pageUploading 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.

pageBrowsing GenomespageBrowsing 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.

pagecgMLST 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.

pageCreating A CollectionpageUsing The Interactive Collection Views