# A Brief Tour of Pathogenwatch 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.

Pages accessible via Genomes, Collections, and Upload menu options

1. [**Browse Genomes**](#browse-and-search-genomes) **by Organism:** All available organisms are listed. 2. [**Search**](#browse-and-search-genomes) **an Organism's genomes:** Filter and select from all publicly-available genomes in the platform, plus any private genomes available to you. 3. **Create** [**Saved Searches**](/pathogenwatch/how-to-use-pathogenwatch/browsing-and-viewing-genomes/browsing-searching-genomes.md#saving-a-search)**:** Save the Search parameters and the search will show on your "Browse Genomes" page. 4. **View a genome's** [**Genome Report**](/pathogenwatch/how-to-use-pathogenwatch/browsing-and-viewing-genomes/genome-reports.md): From the Genomes page or within the Interactive Collection View data table, see a summary of each genome and, where available initiate a [cgMLST-based context search](http:///o/-LB6jV5O6hp6O90DAvtu/s/HXfIP1DQQRf1INOFCCsK/~/changes/42/technical-descriptions-of-analyses/cgmlst-clusters) from within the Genome Report to identify closely-related genomes 5. [**Create a Collection**](#create-a-collection) **of selected genomes**: A "collection" is a snapshot in time, a collection of genomes resulting from a search. 6. **Investigate using the** [**Interactive Collection View**](/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/the-interactive-collection-view.md): Use a tree, map, timeline, and data tables containing analysis results & metadata. Identify trends and explore the collection. Download results. 7. [**Upload** ](#uploading-genomes-reads)**Genomes & Metadata\***: Add genomes, reads, and metadata to your private account 8. [**Share**](/pathogenwatch/how-to-use-pathogenwatch/collections/creating-sharing-collections.md#sharing-your-collection)**\***: Share a collection. Download trees, images, and genome reports. \**permissions may vary by Initiative.* ### Browse & Search Genomes
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: * Set [Search filters](/pathogenwatch/how-to-use-pathogenwatch/browsing-and-viewing-genomes/browsing-searching-genomes.md#using-filters) * Create a [Saved Search](/pathogenwatch/how-to-use-pathogenwatch/browsing-and-viewing-genomes/browsing-searching-genomes.md#saving-a-search) to reuse your filtering parameters * View a genome's detailed [Genome Report](/pathogenwatch/how-to-use-pathogenwatch/browsing-and-viewing-genomes/genome-reports.md) * Select genomes to [create a Collection](/pathogenwatch/how-to-use-pathogenwatch/collections/creating-sharing-collections.md#creating-a-collection).

Filters, Genome Reports, and Saving Searches on the Genomes Page

### Create a Collection Select genomes using the tick boxes. You can select "All in this search" if the search returned <5000 genomes, but only up to 2000 genomes can go into a collection. 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 [Interactive Collection View](#the-interactive-collection-view).

Selecting Genomes & Creating a Collection on the Genomes page

## Notes about Collections * 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. ## The Interactive Collection View Creating a collection or opening a collection from the Collections page brings up the [Interactive Collection View](/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv.md), displaying all genomes in the collection. Follow along with a short [tutorial ](/pathogenwatch/getting-started/interactive-collection-view-tutorial.md)to gain familiarity. ### Tree, Map, Tables & Timeline * [**Tree**](/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/tree-panel.md): a [core distance-based](/pathogenwatch/technical-descriptions-of-analysis-tools/trees-clustering-and-context-search/core-genome-tree.md) neighbour-joining tree, viewed using Phylocanvas (top left) * 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. * [**Map**](/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/map-panel.md): shows all genomes in the collection that have a location associated with them (top right) * [**Data Tables**](/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/data-tables.md) (Metadata & Analysis Results)**,** & [**Timeline** ](/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/timeline.md)(bottom) ### Explore the Collection * [**Map** ](/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/map-panel.md)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. * [**Tree** ](/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/tree-panel.md)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. * [**Metadata blocks**](/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/tree-panel.md#adding-and-editing-metadata-blocks) 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. * [**User-uploaded metadata**](/pathogenwatch/how-to-use-pathogenwatch/uploads-and-folders/genome-uploads-folders.md#metadata) is displayed in the main tab. * [**Typing Assignments**](/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping.md) are provided for each species as applicable. **MLST** is available for all supported species while species-specific schemes are also provided. These include [**Genotyphi**](/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/genotyphi.md#about-genotyphi) for *Salmonella* *typhi* (as in this collection) and [NG-MAST](/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/ng-mast.md) (*Neisseria gonorrhoea*-specific). * [**Antimicrobial Resistance (AMR)**](/pathogenwatch/technical-descriptions-of-analysis-tools/antimicrobial-resistance-prediction/pw-amr.md) 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. * [**Searching for genomes**](#browse-and-search-genomes) **of interest within the collection** can be done with The [Search-and-Filter Bar ](/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/searching-genomes-in-a-collection.md#the-search-and-filter-bar)at the top. * [**Context Search**](/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/context-search.md) **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. #### Change colours to see trends in timeline and other panels

View Timeline, View Legend, Change Colour Column

### Share & Download In some cases, you can download typing, AMR, core similarity and more for local exploration, using the`Downloads` button in the top right corner of both the [Genome Browser ](/pathogenwatch/how-to-use-pathogenwatch/browsing-and-viewing-genomes/browsing-searching-genomes.md)and the [Interactive Collection View](/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/the-interactive-collection-view.md). * 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). ## Uploading genomes/reads 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 [Uploading New Genomes](#uploading-genomes-reads) section. ![](/files/-LBWjkWupoStj4fk0vk1) ## Learn more Follow the [tutorial](/pathogenwatch/getting-started/interactive-collection-view-tutorial.md) on the next page Explore detailed descriptions and guides to each component in the [How to use Pathogenwatch](/pathogenwatch/how-to-use-pathogenwatch.md) section. Read full descriptions of the underlying analyses & methods in the [Technical Descriptions of Analysis Tools](/pathogenwatch/technical-descriptions-of-analysis-tools.md) section. We also recommend checking the [FAQ ](/pathogenwatch/faq.md)and contacting us. {% content-ref url="/pages/0lrSfr64bpKjeJaaM59I" %} [Interactive Collection View tutorial](/pathogenwatch/getting-started/interactive-collection-view-tutorial.md) {% endcontent-ref %} {% content-ref url="/pages/Bn1UiY9QmCJtwoQdN0ZR" %} [How to use Pathogenwatch](/pathogenwatch/how-to-use-pathogenwatch.md) {% endcontent-ref %} {% content-ref url="/pages/GYlF21lzJnLGpmvIY014" %} [Technical Descriptions of Analysis Tools](/pathogenwatch/technical-descriptions-of-analysis-tools.md) {% endcontent-ref %} {% content-ref url="/pages/MZ27LWy6Vs8L5e1qJnP5" %} [FAQ](/pathogenwatch/faq.md) {% endcontent-ref %} {% hint style="info" %} Email: {% endhint %} --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://cgps.gitbook.io/pathogenwatch/getting-started/a-brief-tour-of-pathogenwatch.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.