Virtool is built for detecting viruses and is capable of detecting other pathogens. Managing collections of pathogen sequences used for this purpose is a key feature of Virtool.

At least one non-empty reference must be created in order to start analyzing samples. One quick way to accomplish this is to install the official plant virus reference.

Install the Official Reference

Instead of starting a virus database from scratch, you can use our official plant virus reference. Doing this will setup up remote connection to the reference on GitHub.

1. Go to the References view

   A message with a button for installing the official reference will be visible if you have not already installed it.

   

2. Click the Install button to begin the installation process

   A new card should appear representing the official reference on your system. It will display a progress bar while the reference is being created locally.

   

   Once the installation process is complete, the reference card should look something like this:

   

3. Click the reference card to view a detail page for the reference

   

Browse OTUs

Once the installation of the official reference is complete, you can browse the OTUs that are included in the reference.

1. Click on the OTUs tab

   You should see something like the following. This is searchable list of all OTUs in the reference.

   The There are unbuilt changes message means you have to build a new index for the reference before you can use it in analyses.

   

2. Search OTUs by their names or abbreviations

   

Build an Index

Before the imported data can be used in analyses, an optimized index must be built. Think of this as a publication or commit step.

1. Go to the Indexes tab in the reference detail view

   

2. Click the Rebuild the index link to prepare an index build

   The Rebuild Index dialog will appear, summarizing the OTU changes that will be included in the index.

   

3. Click the Start button at the bottom of the dialog.

   This will start an index build job. A new index entry will appear with the Building label.

   

4. Wait for the build to complete

   The index will look something like this is when it is ready to use. It will have the Active label.