Collection search
Exploring the genomic neighbourhood for a collection of genomes
This feature is experimental and is not yet available to all users
Build and view the context
Pathogenwatch provides a facility in the collection view for identifying genomic neighbours for a collection of genomes - for instance an outbreak or local surveillance collection. The set of genomes to search against can be selected, along with the maximum linkage threshold - this value can be modified dynamically after the search is completed in order to further refine the context. Once the context has been generated, a new collection is created containing both the original and context genomes.
Selecting the search set
The "Add Context" button can be found in the top right corner of the collection view, and appears as a "+" symbol. Click this will reveal the context selection panel on the right side. This panel consists of four sections, each allowing limitations on the included context:
The threshold selector
The search folders selector
The country selector
The date range selector
The threshold selector can be set from 1-50. Clicking on the button will show the current threshold above it, while dragging it will alter the current setting.
The folder selector shows which folders will be included in the search. Only genomes belonging to those folders will be returned.
The country and time filters can be used to exclude genomes from the search folders for more focussed searches.
Clicking the "Search" button at the bottom of the panel will initiate the search. The search tool will then find the 5000 nearest neighbours and create the linked clusters. Once the search is completed an embedded cluster viewer will be shown, and thresholds used to refine the set of selected genomes. Adding the new genomes will initialise a new collection for further exploration. Note that the original collection will be unmodified.
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