This tutorial assumes you have already done the following:

• created a sample
• created and built a reference
• created a subtraction
• installed HMM profiles and annotations

You will use these data sources to run a workflow for discovering potential novel virus sequences in a sample.

Start an Analysis Job

1. Navigate to the Samples view

   

2. Click on a sample

   You will see the general information for the sample.

   

3. Navigate to the Analyses tab

   You will see a list of analyses for the sample. The sample Test A has one PathoscopeBowtie analysis already complete.

   

4. Click the button to open the analyze dialog

   

5. Complete the analyze form

   Select the NuVs algorithm, a reference against which to eliminate known sequences. If you select multiple reference, a separate job will be created for each one.

   

6. Click the Start button

   The dialog will close and you will immediately see your new analysis appear in the list. NuVs can take significantly longer than Pathoscope to complete.

   

   When the analysis is complete, the list item will look like this:

   

7. Navigate back to the Samples view

   The sample entry will be tagged to show that a NuVs analysis has been completed.

   

View NuVs Results

1. Navigate to the Analyses tab for a sample

   

2. Click on the NuVs analysis item

   The list shows assembled sequence fragments (contigs) that may be part of a novel virus.

   

   In the NuVs workflow, sample libraries are assembled into contigs. Open reading frames (ORFs) are calculated from these and potential protein annotations are assigned using profile HMMs.

   

3. Click the Filter ORFs button.

   This will toggle the visibility of ORFs with no HMM annotations, which are hidden by default.

   

4. Click the Filter Sequences button

   This will toggle the visibility of contigs without significant HMM hits, which are filtered out by default.

   

5. Click the BLAST at NCBI button to BLAST the contig at NCBI

   

6. Wait for the BLAST search to complete

   Part of interpreting NuVs results is BLASTing contigs to make sure they are truly unknown. The BLAST results for this sequence show it is likely a contamination from a technician.