This tutorial assumes you have already
You will use these data sources to run a workflow 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 view 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 thebutton to open the analyze dialog
Select the analysis parameters
Select the Pathoscope workflow, a subtraction, and one or more references to search against. Selecting more than one reference will start a separate analysis job for each reference.
Click thebutton to start the job
The dialog will close and you will immediately see your new analysis appear in the list.
When the analysis is complete it will look like this:
Go back to the Samples view
The sample item is tagged to show that a Pathoscope analysis has been completed.
Navigate to the analysis tab for a sample.
Click on an analysis
The detail for the analysis will be displayed.
View the mapping overview
This shows how many sample reads were mapped to the reference (eg. Plant Viruses) and the subtraction (eg. Arabidopsis thaliana).
View the result list
The list shows the viruses Virtool thinks are likely to be in the sample. Each identified OTU is listed and be expaned to show the coverage chart and detailed numbers for each isolate and sequence.
Use the mouse or the w and s keys to select OTUs
Click thebutton to show all OTUs
By default, OTUs with low coverage or weight (relative abundance) are filtered out. The OTUs shown here would normally be filtered out:
Clicking an OTU shows coverage charts for the isolates
Click theto show all isolates
By default, isolates with low coverage or wheight are filtered out.
Virtool excels at detecting virus infections at the isolate-level. In this case, it is clear that Isolate 1050-02 is the infecting isolate rather than Isolate GRSPaV-MG, which would normally be filtered out.