Run NuVs Updated February 5, 2020

This tutorial assumes you have already created a sample, created and built a reference, created a subtraction, and installed HMM profiles and annotations. You will use these data sources to run a bioinformatic pipeline for discovering potential novel virus sequences in a sample.

Start an Analysis Job

Navigate to the Samples view.

Samples List View

Click on a sample. You will see the general information for the sample.

Sample General

Navigate to the Analyses tab to see a list of analyses for the sample.

“Empty Analysis List

Click to open the analysis creation dialog, select NuVs and a reference against which to eliminate known sequences, and click Start.

“Analysis Dialog”

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

“Analysis Running”

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

“Analysis Complete”

In the Samples view, you will notice the sample entry is tagged to show that a NuVs analysis has been completed.

“NuVs Sample Tag”

View NuVs Results

Carrying on from the previous section, click on your recently created analysis. The list shows sequence fragments (contigs) that may be part of a novel virus. Filtered

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

By default, ORFs with no HMM annotation are hidden. You can toggle the visibility of these by clicking the Filter ORFs button. Unfiltered ORFs

Contigs without significant HMM hits are filtered out by default. Click Filter Sequences to show all contig sequences. Unfiltered Sequences

Part of interpreting NuVs results is BLASTing contigs to make sure they are truly unknown. You can BLAST contigs by clicking BLAST at NCBI. BLAST at NCBI

The BLAST results for this sequence show it is likely a contamination from a technician. BLAST Results