This tutorial assumes you have already

• created a sample
• created and built a reference
• created a subtraction

You will use these data sources to run a workflow for detecting, in a sample, known viruses from your virus database.

Start a Pathoscope Job

1. Navigate to the Samples view

   

2. Click on a sample

   You will see the general information view for the sample.

   

3. Navigate to the Analyses tab

   You should see an empty list if you haven’t already created an analysis for this sample.

   

4. Click the button to open the analyze dialog

   

5. 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.

   

6. Click the Start button 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:

   

7. Go back to the Samples view

   The sample item is tagged to show that a Pathoscope analysis has been completed.

   

View Pathoscope Results

1. Navigate to the analysis tab for a sample.

   

2. Click on an analysis

   The detail for the analysis will be displayed.

   

3. View the mapping overview

   This shows how many sample reads were mapped to the reference (eg. Plant Viruses) and the subtraction (eg. Arabidopsis thaliana).

   

4. 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.

   

5. Use the mouse or the w and s keys to select OTUs

6. Click the Filter OTUs button 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:

   

7. Clicking an OTU shows coverage charts for the isolates

   

   • Deep, wide coverage of an isolate is indicative of an infection.
   • Shallow, wide, and broken coverage is suggestive of intra-plate contamination. Hits due to contamination also typically have low weights.
   • Isolates with high weight, and deep localized coverage are typical of low-complexity or host-similar regions in the isolate genome and do not indicate true infections.

8. Click the Filter Isolates to 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.