Find QIAseq xHYB AMR Markers

The Find QIAseq xHYB AMR Markers template workflow trims reads and detects antimicrobial resistance (AMR) markers.

It is suitable for data generated with the QIAseq xHYB AMR Panel.

QIAGEN reference data set

The QIAseq xHYB AMR Panel 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 QIAseq xHYB AMR Markers 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) | Find QIAseq xHYB AMR Markers (Image ar_quantify_16_n_p)

Launch the workflow and step through the wizard.

  1. Select the sequence list(s) containing the reads to analyze and 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 3.86). Click on Next.
  3. Choose whether batch units should be defined based on organization of the input data, or by provided metadata (figure 3.87). 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 reference marker database (figure 3.88). Click on Next.
  6. Verify or select control genes (figure 3.89). Click on Next.
  7. Specify the trim settings (figure 3.90) and click on Next.
  8. Finally, select a location to save outputs to and click on Finish.

Image find_qiaseq_reference
Figure 3.86: Select reference data set.

Image find_qiaseq_batching
Figure 3.87: Define batch units.

Image find_qiaseq_marker
Figure 3.88: Select the reference marker database.

Image find_qiaseq_controlgenes
Figure 3.89: Select control genes.

Image find_qiaseq_trim
Figure 3.90: Trim settings.

Tools in the workflow and outputs generated

The workflow Find QIAseq xHYB AMR Resistance consists of the below mentioned tools. See figure 3.91 for a full overview of the workflow.

Image find_qiaseq_layout
Figure 3.91: Layout of the QIAseq xHYB AMR Markers workflow.

The tools included in the workflow are:

The outputs provided by this workflow are: