Analyze QIAseq xHYB Viral Panel Data (Human host)

The Analyze QIAseq xHYB Viral Panel Data (Human host) template workflow trims reads, performs taxonomic profiling, and calls viral variants. It is suitable for analysis of samples from human hosts generated with the QIAseq xHYB viral panels:

To analyze non-human samples, you can create a copy of the workflow and edit it to fit your specific application, see Since the workflow element Map Reads to Human Control Genes is relevant for human data only, you should delete this. In addition, if a host genome is not relevant for you application, open the Taxonomic Profiling workflow element, and uncheck Filter host reads.
Once the workflow copy is customized, you can install it to make it available from the Toolbox, see

QIAGEN reference data set

The QIAseq xHYB Viral Panels reference data set is available from QIAGEN Sets Reference Data Library accessible via References (Image referencemanager_16_n_p) in the top Toolbar.

Like the template workflow, the reference data set is designed for human samples. It contains both a human host taxonomic profiling index, and a sequence list with human control genes for use in the workflow step Map Reads to Human Control Genes.

For analysis of non-human data, if a host is relevant for your application, you can create a host taxonomic profiling index from your host reference genome using Create Taxonomic Profiling Index, see Create Taxonomic Profiling Index.

Launching the workflow

The Analyze QIAseq xHYB Viral Panel Data (Human host) 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 (Human host) (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 2.71). Click on Next.
  3. Choose whether batch units should be defined based on organization of the input data, or by provided metadata (figure 2.72). 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 2.73) 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 (2.74). 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 2.75).
  11. Specify Low Frequency Variant Detection settings, see figure 2.76.
  12. Finally, select a location to save outputs to and click on Finish.

Image analyze_qiaseq_reference
Figure 2.71: Select reference data set.

Image analyze_qiaseq_batching
Figure 2.72: Define batch units.

Image analyze_qiaseq_taxpro
Figure 2.73: Select viral taxonomic profiling index.

Image analyze_qiaseq_viral_database
Figure 2.74: Select one or more viral reference databases.

Image analyze_qiaseq_filter
Figure 2.75: Set taxonomic profiling parameters.

Image analyze_qiaseq_low_freq
Figure 2.76: Low frequency variant detection settings.

Workflow tools and outputs

The Analyze QIAseq xHYB Viral Panel Data (Human host) template workflow consists of the following tools.

The sample-specific outputs provided by this workflow are:

The combined outputs provided by this workflow are: