This tutorial assumes you have already created a sample, created and built a reference, and created a subtraction. You will use these data sources to run a bioinformatic pipeline for detecting, in a sample, known viruses from your virus database.
Navigate to the Samples view.
Click on a sample. You will see the general information for the sample.
Navigate to the Analyses tab. You should see an empty list if you haven’t already created an analysis for this sample.
Click to open the analysis creation dialog. Select PathoscopeBowtie and a refernece to search against, and then click Start.
The dialog will close and you will immediately see your new analysis appear in the list.
When the analysis is complete, the list item will look like this:
In the Samples view, you will notice the sample entry is tagged to show that a Pathoscope analysis has been completed.
Carrying on from the previous section, click on your recently created analysis. The list shows the viruses Virtool thinks are likely to be in the sample.
By default, viruses with low coverage or weight (relative abundance) are filtered out. They can be made visible by clicking .
Clicking a virus shows sequencing coverage charts for the isolates that may be in your sample.
Filtering of low weight and coverage isolates is toggled by clicking . Virtool excels at detecting virus infections at the isolate-level. In this case, it is clear that Isolate Q65b is the infective isolate rather than Isolate Nanjing.