Creating A Collection

About Collections

Pathogenwatch collections are a way of creating meaningful groups of genomes for comparing and sharing with collaborators and the communities. Typical uses of collections include:

  • Supplementing publications,

  • Providing an interactive public interface to a large-scale survey,

  • Storing the results of a particular study or investigation for future reference,

  • Highlighting an observation and sharing with public health colleagues.

Creating A Collection

Collections are created by first selecting assemblies in the Genomes window - for a quick example visit the "Getting Started" tutorial or the "Browsing Genomes" documentation page. If you are creating a collection of freshly uploaded assemblies, these will already be displayed for selection. Once the required assemblies are selected, click the "Selected Assemblies" button and then "Create Collection".

At this point, you are presented with the option of filling in a description of the collection. The fields include:

  • Title - This will be included in the collection URL.

  • Description - A short description of the collection, perhaps to explain to other people what it is for.

  • PMID/DOI - The PubMed or DOI identifier if it is linked to a publication.

Finally, click "Create Now" and you will be taken to the Collection View. For a subset of species, listed under thee "SNP tree supported" filter, a tree will be calculated using an internal method described in "Core Genome Tree". If the tree of the collection has not been previously calculated, it make a few seconds to a few minutes to create, depending on the server load and collection size.

The URL of the collection is permanent, and is composed of a unique unpredictable identifier (required) and the title of the collection (optional, for readability). If the tree is taking time to build, it's safe to close the window and return later.

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