Welcome to Pathogenwatch
Pathogenwatch provides a platform for comparing pathogen genomes from around the world, integrating diverse data sets with rich representations.
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.
Customisations
Some initiatives have customised features that have been specifically tailored (e.g., PATH-SAFE multi-organisation initiative). These extended and adapted features have been highlighted in the documentation by the following symbol (!), as shown below, and are only made accessible to users signed in with an account linked to that initiative.
Notes for specific initiatives (e.g. PATH-SAFE) appear in a (!) callout block like this message. These have been included to relay the extended capabilities of the application for those users.
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.
Antibiotic resistance prediction.
Interrogate the database using cgMLST-based clustering.
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.
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 & 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.
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