A Brief Tour of Pathogenwatch
Last updated
Last updated
More detail on the various concepts and functionalities listed below can be found through these documentation pages.
Below the image, click each list item to jump to a description.
by Organism: All available organisms are listed.
an Organism's genomes: Filter and select from all publicly-available genomes in the platform, plus any private genomes available to you.
Create : Save the Search parameters and the search will show on your "Browse Genomes" page.
View a genome's : From the Genomes page or within the Interactive Collection View data table, see a summary of each genome.
of selected genomes: A Collection is a snapshot in time, a collection of genomes resulting from a search.
Investigate using the : Use a tree, map, timeline, and data tables containing analysis results & metadata. Identify trends and explore the Collection. Download results.
Genomes & Metadata*: If "Upload" is an option for you, add genomes, reads, and metadata.
*: Share a Collection. Download trees, images, and Genome Reports.
*permissions may vary by Initiative.
Select an organism on the Browse Genomes page to search for all of that species' genomes available to you. Here we will show selecting Salmonella enterica. On the Genomes page that opens:
Select genomes using the tickboxes. You can select "All in this search" if the Search returned <5000 genomes, but only up to 2000 genomes can go into a Collection.
Collections are the easiest way of sharing data with colleagues or the general public. Some Collections are pre-built, and accessible from the Collections page.
Collections you create are shown in the "My Collections" section on the Collections page.
The Interactive Collection View's URL is permanent, though the title text is optional. You can bookmark it in your browser to return later.
When you create a Collection, the tree is not created automatically. If it is possible to create a tree for the selected organism, then a "generate tree" button will be shown.
FASTAs of the assembly, and an accompanying GFF-format file with Pathogenwatch features included.
A tree can be downloaded as a Newick file (right-click).
Set
Create a to reuse your filtering parameters
View a genome's detailed
Select genomes to .
When you have (1) selected a set of desired genomes, (2) open the "Selected Genomes" basket and click the (3) "Create Collection" button. (4) Give your Collection a name and description, and (5) click Submit. This brings up the .
Creating a Collection or opening a Collection from the Collections page brings up the , displaying all genomes in the Collection. Follow along with a short to gain familiarity.
: a neighbour-joining tree, viewed using Phylocanvas (top left)
: shows all genomes in the Collection that have a location associated with them (top right)
(Metadata & Analysis Results), & (bottom)
displaying geographic distribution of genomes in the Collection. Select a subset by clicking or using the map region filter or viewport filter, and see them highlighted in the tree and data tables.
showing the relationships of all genomes in the Collection, and can be explored in various ways, including zooming, viewing subtrees (right-click), changing the layout mode, labels, or node size. Try increasing the node size to make selected genomes clearer.
can be displayed next to the leaves (genomes) on the tree by clicking a column header of interest. Adjust the text size in the Tree Panel to help with readability.
is displayed in the main tab.
are provided for each species as applicable. MLST is available for all supported species while species-specific schemes are also provided. These include for Salmonella typhi (as in this collection) and (Neisseria gonorrhoea-specific).
predictions from are displayed in the Antibiotics/SNPs/Genes tables accessed via the selector in the corner of the table region. Resistance is given as "Unknown/Intermediate/Resistant -> White/Yellow/Red". The same colours are used to visualise the resistance profiles in the tree and map when selected. Click on different antibiotics and resistance genes to see this in practice.
of interest within the Collection can be done with The at the top.
for related genomes outside the Collection: This feature is available to some Initiatives, and is accessed via the "plus button" (top right), which brings up options to search desired folders, countries, timeframes, and allele distance thresholds.
In some cases, you can download typing, AMR, core similarity and more for local exploration, using theDownloads button in the top right corner of both the and the .
You can upload your own genomes, with accompanying metadata, for analysis and comparison with the Pathogenwatch public assemblies via the Uploads tab. For a complete explanation and examples see the section.
Note for PATH-SAFE initiative: are handled externally to the Pathogenwatch application's user interface, hence the upload functionality is not required (and has been disabled).
Follow the on the next page
Explore detailed descriptions and guides to each component in the section.
Read full descriptions of the underlying analyses & methods in the section.
We also recommend checking the and contacting us.
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