Analyze QIAseq xHYB Viral Panel Data (Human host)

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

QIAGEN reference data set

The QIAseq xHYB Viral Panels and QIAseq xHYB HepC Panel Reference Data Sets contain reference data relevant to this template workflow. The data can be downloaded and managed using the Reference Data Manager. To download the data, open the Reference Data Manager by clicking on the Manage Reference Data (Image referencemanager_16_n_p) button in the top Toolbar, go to the QIAGEN Sets Reference Data Library tab, and locate the relevant set. Data from the Reference Data Sets that have not already been downloaded can be downloaded when the workflow is run.

Like the template workflow, the Reference Data Sets are designed for human samples. They include 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 samples not from human hosts: If a non-human 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.

Workflow customization

You can create a copy of the template workflow and edit it to fit your specific application, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Template_workflows.html. This could be useful e.g., in the following cases:

Launching the workflow

The Analyze QIAseq xHYB Viral Panel Data (Human host) template workflow is available at:

        Workflows | 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.
  2. Select a reference data set or select "Use specified data elements". The latter runs the workflow using default elements, which can be viewed by clicking the "workflow roles" text just above the option.
  3. Define batch units. For details, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Running_part_workflow_multiple_times.html.
  4. Check that batching is as intended.
  5. Verify or select the viral taxonomic profiling index (figure 2.33).
  6. Verify or select the host taxonomic profiling index.
  7. Select the viral reference database(s). If in the first step you selected e.g., the QIAseq xHYB Viral Panels reference set, you can now select which of the available viral reference databases from that set to apply (2.34). If you chose to use the specified data elements, select a reference database.
  8. Verify or select the control genes.
  9. If your reads contain adapters, add an appropriate Trim adapter list (see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Adapter_trimming.html). This is optional and not needed if the QIAseq xHYB Microbial Hyb Kit was used.
  10. Specify Low Frequency Variant Detection settings, see figure 2.35.
  11. Specify Extract Consensus sequence settings (figure 2.36).
  12. In the "Create Full Sample Report" step various summary items have been set. These are guidelines to help evaluate the quality of the results.
  13. Finally, select a location to save outputs to.

Image analyze_qiaseq_taxpro
Figure 2.33: Select viral taxonomic profiling index.

Image analyze_qiaseq_viral_database
Figure 2.34: Select one or more viral reference databases.

Image analyze_qiaseq_low_freq
Figure 2.35: Low frequency variant detection parameters.

Image analyze_qiaseq_extract_consensus
Figure 2.36: Extract Consensus Sequence parameters.

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: