Fig. 1. Workflow of the Typhi Pathogenwatch application.

Input assemblies or sequence reads and metadata files can be uploaded via drag-and-drop onto the Upload page. Once the analyses completed, the genomes are listed on the Genomes page with Pathogenwatch outputs for speciation and MLST. Clicking on a genome name on the list pops up a Genome Report. The user can create collections of genomes. The Collection view displays the user genomes clustered by genetic similarity on a tree, their location on a map, a timeline, as well as tables for metadata, typing and AMR. The Population view displays the user genomes by their closest reference genome in the population tree. Clicking on one of the highlighted nodes (purple triangles) opens the Population subtree view, which contextualizes the user genomes with the closest public genomes.