Welcome to Pathogenwatch

Overview and Key Links.

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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 Genomes
Browsing 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
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Announcements

Last modified 11mo ago