Install Reference Updated February 5, 2020

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.

Go to the References view. If you have not yet installed the official reference, you should see this:

“Official Reference Placeholder”

Click the Install button to begin the installation process. A new card should appear representing the official reference on your system.

“Official Reference Installing”

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

“Reference Installation Complete”

Clicking on the reference card will bring you to a detail page for the reference.

“Installed Official Reference Detail Page”

Browse OTUs

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

Click on the OTUs tab and you should see something like the following:

The OTUs tab

You can search OTUs by their names or abbreviations.

Search OTUs

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

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.

Look for the Indexes tab in the reference detail view.

“Indexes tab”

Click the Rebuild the index link to start preparing an index build.

“Empty Indexes List”

An index creation dialog describing the changes to be built will appear.

“Index Creation Dialog Top” “Index Creation Dialog Bottom”

Click the Start button at the bottom of the dialog to start an index build job. A new index entry will appear with the Building label:

“An index building”

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

“A ready index”