This tutorial assumes you have already done the following:
You will use these data sources to run a workflow for discovering potential novel virus sequences in a sample.
Navigate to the Samples view
Click on a sample
You will see the general information for the sample.
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.
Click thebutton to open the analyze dialog
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.
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:
Navigate back to the Samples view
The sample entry will be tagged to show that a NuVs analysis has been completed.
Navigate to the Analyses tab for a sample
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.
This will toggle the visibility of ORFs with no HMM annotations, which are hidden by default.
This will toggle the visibility of contigs without significant HMM hits, which are filtered out by default.
Click thebutton to BLAST the contig at NCBI
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.