Browsing Genomes

How to navigate and select genomes in the genome browser.

The Genome Page

Default View

All assemblies currently available from pathogenwatch can be accessed via the "Genomes" tag near the top right. If you are logged in your private assemblies will also be displayed.

Upload View

If you arrive on the Genome page as a result of uploading a set of genomes, the uploaded assemblies are presented automatically, and tagged as a single group in the bottom left.

If you are logged in, your previous uploads will also be displayed here.

Click the assembly name to view a detailed report on it.

Selecting Assemblies

Pathogenwatch uses a "shopping basket"-like approach to building a selection of assemblies for comparison. The core method is as follows, for more detailed instructions on each part see the sections below:

  1. You search all the available assemblies by using with the filters on the left.

  2. Then select the assemblies you wish to investigate further in the middle using the checkboxes or map select tool.

  3. These are added to the "Selected Genomes" basket on the top right.

  4. Repeat (1) & (2) until you have all the assemblies you want in the "Selected Genomes" set.

Once you have built a selection, click "Selected Genomes" to download analysis data about them, or create a "Collection View".

The Assembly List

The central panel shows all the assemblies currently meeting the filter criteria. By default this is all assemblies, and showing the List View. You can also switch to a map display, or view graphs of assembly statistics.

List View

Each row in the list view corresponds to an uploaded assembly, with the checkbox to mark it's inclusion in the "Selected Genomes". Clicking on the assembly 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 assemblies still in the list.

Map View

Assemblies with location data are displayed in the map view. Clicking on individual assemblies will bring up the Assembly Report. Groups of assemblies can be selected for inclusion in the Selected Genomes by using the map selection tool in the top right, outlining the area of interest, and ticking genomes in the pop up box.

Assembly Metrics

Press the "Stats" button to view graphs of assembly metrics for the current list of assemblies. These include genome length, contig number, GC ratio, N50 and non-ATCG. Each dot represents an assembly, and clicking on it will bring up an assembly report.

Using Filters

On the left hand side of the page is the Filter Panel. From here you can require assemblies to have specific attributes. The attributes are grouped by category, such as species, AMR, country or upload time. Within each category the available attributes are indicated as purple boxes with the number of associated assemblies indicated.

One attribute can be selected from each category at a time. When you select an attribute the assembly list will be automatically filtered to only include those with that attribute (e.g. Ampicillin resistance). The date filter is a special case, and allows you to select assemblies from within a time range.

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