Welcome to Pathogenwatch

Pathogenwatch provides a platform for comparing pathogen genomes from around the world, integrating diverse data sets with rich representations.

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

Introduction

Pathogenwatch is a user-friendly web platform empowering researchers and public health professionals to analyse and visualise genomic data from microbial pathogens. Designed to streamline pathogen surveillance, it integrates advanced tools for resistance gene detection, phylogenetic analysis, and outbreak tracking, with interactive visualisations and access to global databases. By combining cutting-edge genomic analysis with seamless data sharing, Pathogenwatch enables faster, more informed decision-making to combat antimicrobial resistance and monitor the spread of infectious diseases worldwide.

To get started, sign in and then take a "Brief Tour of Pathogenwatch", or learn even more in the "How to use Pathogenwatch" pages.

Upload microbial genomes to initiate a suite of automated analyses

• Your submitted genome data is kept private unless requested. Instructions for this are provided in the Genome Uploads section.

• 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.

Genome Uploads & Folders

Browse published genomes and collections 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 & Searching 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 & Context Searching

Create & interact with collections for a deeper view

• Create a single collection integrating public genomes with your own.

• Make the collection public to share your insights with other researchers.

• The powerful Interactive Collection View integrates the CGPS Phylocanvas tree panel with a map panel and data tables, along with a query tool for highlighting genomes with particular features.

Creating & Sharing CollectionsUsing The Interactive Collection View

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