Analyze QIAseq xHYB Viral Panel Data

The Analyze QIAseq xHYB Viral Panel Data template workflow trims reads, performs taxonomic profiling, and calls viral variants.

It is suitable for data generated with the QIAseq xHYB viral panels:

QIAGEN reference data set

The QIAseq xHYB Viral Panels reference data set is available from QIAGEN Sets Reference Data Library accessible via References (Image references_icons) in the top Toolbar.

Launching the workflow

The Analyze QIAseq xHYB Viral Panel Data workflow is at:

        Toolbox | Template Workflows (Image workflow_group) | Microbial Workflows (Image mgm_folder_closed_flat_16_h_p) | QIAseq Analysis (Image qiaseq_workflows_folder_closed_16_n_p) | Analyze QIAseq xHYB Viral Panel Data (Image viral_hybrid_capture_16_n_p)

Launch the workflow and step through the wizard.

  1. Select the sequence list(s) containing the reads to analyze. Click on Next.
  2. Select a reference data set or select "Use the default reference data" to configure the reference data elements individually in subsequent wizard steps (figure 3.79). Click on Next.
  3. Choose whether batch units should be defined based on organization of the input data, or by provided metadata (figure 3.80). For information on how to use metadata when running part of a workflow multiple times, see
  4. Next, you can review the batch units resulting from your selections above. Click on Next.
  5. Verify or select the viral taxonomic profiling index (figure 3.81) and click on Next.
  6. Verify or select the host taxonomic profiling index and click on Next.
  7. Select the viral reference database(s). If in the first step you selected the QIAseq xHYB Viral Panels reference set, you can now select which of the available viral reference databases from that set to apply (3.82). If you chose to use the default reference data, select a reference database and click on Next.
  8. Verify or select the control genes and click on Next.
  9. Specify the trim settings.
  10. Specify Taxonomic Profiling settings (figure 3.83).
  11. Specify Low Frequency Variant Detection settings, see figure 3.84.
  12. Finally, select a location to save outputs to and click on Finish.

Image analyze_qiaseq_reference
Figure 3.79: Select reference data set.

Image analyze_qiaseq_batching
Figure 3.80: Define batch units.

Image analyze_qiaseq_taxpro
Figure 3.81: Select viral taxonomic profiling index.

Image analyze_qiaseq_viral_database
Figure 3.82: Select one or more viral reference databases.

Image analyze_qiaseq_filter
Figure 3.83: Set taxonomic profiling parameters.

Image analyze_qiaseq_low_freq
Figure 3.84: Low frequency variant detection settings.

Tools in the workflow and outputs generated

The workflow Analyze QIAseq xHYB Viral Panel Data consists of the below mentioned tools. See figure 3.85 for a full overview of the workflow.

Image analyze_qiaseq_layout
Figure 3.85: The Analyze QIAseq xHYB Viral Panel Data workflow layout.

The tools used in this workflow are:

The sample-specific outputs provided by this workflow are:

The combined outputs provided by this workflow are: