Browsing & Searching Genomes
Genomes can be searched using filters. Searches can be saved.
The Genomes Page
All genomes currently available to you in Pathogenwatch can be accessed via the "Genomes" menu item, including any private genomes (if you are logged in).
https://rc.pathogen.watch/genomes
If you have saved any searches, your "Saved Searches" will show at the top of the page.
If other users have shared saved searches with you, those will show next in "Shared Searches."
Next is the "Browse Genomes by Organism" section, which lists organisms, grouped by WHO Priority.
On this page, you can delete saved searches if you own them.
Clicking on an organism name or a saved search card brings you to the Browse Genomes page.
The Browse Genomes Page
On the Browse Genomes page, you have a Filter Panel (left), a Genome List, and buttons for "Save search" and "Selected Genomes."
the organism name is a dropdown list organised by WHO priority, just like on the Genomes Page. From here you can switch to a different organism.
The Genome List
The central panel shows all the genomes currently meeting the filtering criteria. By default, this is all of the selected organism's genomes that are available to you.
Each row in the list view corresponds to an uploaded genome, with the checkbox to mark it's inclusion in the "Selected Genomes". Clicking on the genome name will bring up the Genome Report with detailed information on the bioinformatics outputs and metadata. The columns are sortable by clicking on the headers. This may take some time if there are many genomes still in the list.
Using Filters
On the left hand side of the page is the Filter Panel. From here you can search for genomes with specific attributes. The attributes are grouped by category, such as MLST, Resistance, Country, Folder, and Date. Filtering options will appear when some of the genomes currently in the list contain information relevant to the filter (i.e. you cannot filter by date if none of the genomes have Date metadata associated with them).
When you select an attribute, the genome list will automatically apply the filter, listing only the genomes that meet your filtering criteria.
Note that the Date filter allows you to choose whether you want to filter by the Metadata date field or the date the genome was uploaded.
Selecting Genomes
Pathogenwatch uses a "shopping basket"-like approach to building a selection of genomes for comparison.
Set filters to search for genomes meeting your desired criteria.
Select the genomes using the tickboxes.
These are added to the "Selected Genomes" basket on the top right.
Repeat (1) & (2) until you have all the genomes you want in the "Selected Genomes" set.
Saving a Search
Selecting specific genomes allows you to create a collection. However, that collection will be static, and new genomes won't be added to it automatically.
Searches are dynamic query results across Folders. A Saved Search will always return a list of genomes that meet the search criteria, and when new genomes meeting those criteria are uploaded, those new genomes will show in the search results.
Running a search, which can be as simple as selecting an organism or as complex as applying all available filters. Selecting a set of filters will always pull from all genomes available to you.
Once you have set your filtering criteria, click the "Save search" button to make it easy to repeat the search in the future.
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