# Browsing & Searching Genomes Genomes can be searched using [filters](#using-filters). Searches can be [saved](#saving-a-search). ## 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). 1. At the top is the "[**Browse Genomes by Organism**](#the-browse-genomes-page)" section, which lists organisms, grouped by WHO Priority. 2. Beneath that is the full genome list, covering all species that Pathogenwatch provides analytics for, including viral and fungal species. 3. The next section covers saved searches: 1. First any searches you have saved will be shown under "[**Saved Searches**](#saving-asearch)**".** 2. If other users have shared saved searches with you, those will show next in "**Shared Searches.**" 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](#using-filters) (left), a [Genome List](#the-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](/pathogenwatch/how-to-use-pathogenwatch/browsing-and-viewing-genomes/browsing-searching-genomes.md#using-filters) 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](/pathogenwatch/how-to-use-pathogenwatch/browsing-and-viewing-genomes/genome-reports.md) with detailed information on the bioinformatics outputs and metadata. The columns can be sorted by clicking on the headers. {% hint style="info" %} Search for a list of genomes by copy and pasting the list (one per line) into the "Search Name" box. {% endhint %} ### Searching by Name, Accession or Collection Genomes can be searched by name, run accession, sample accession, project accession, and the URL of a [Pathogenwatch collection](/pathogenwatch/how-to-use-pathogenwatch/collections.md), using the "Search Name" box above the filter selectors. To search for a list of genomes, create the list of names in a text editor or spreadsheet with one name per line, and then copy and paste the list into the search box. This will automatically format the list for submission. Then click search or hit enter to submit the search. Note that this will not return genomes if they have not been assigned the selected species. {% hint style="danger" %} We strongly recommend not including double quotes or commas in sample names. While the search box will handle this scenario, it may break many other systems. {% endhint %} ### 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. {% hint style="info" %} Click an individual genome name to view the detailed [report](/pathogenwatch/how-to-use-pathogenwatch/browsing-and-viewing-genomes/genome-reports.md). {% endhint %} ## Selecting Genomes Pathogenwatch uses a "shopping basket"-like approach to building a selection of genomes for comparison. 1. Set filters to search for genomes meeting your desired criteria. 2. Select the genomes using the tick boxes. 3. These are added to the "Selected Genomes" basket on the top right. 4. Repeat (1) & (2) until you have all the genomes you want in the "Selected Genomes" set. {% hint style="info" %} Once you have built a selection, click "Selected Genomes" to download analysis data about them, or [create a collection](/pathogenwatch/how-to-use-pathogenwatch/collections/creating-sharing-collections.md). {% endhint %} ## Downloading data Once you have selected a set of genomes, metadata and analysis results files can be downloaded via the basket in the top right. Clicking the `Download` button will bring up a list of downloads, with analysis downloads split by species.
## 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. {% hint style="info" %} Saved searches can be deleted by using the bin icon in the search card. {% 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/how-to-use-pathogenwatch/browsing-and-viewing-genomes/browsing-searching-genomes.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.