Find QIAseq xHYB AMR Markers (Human host)

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

It is suitable for analysis of samples from human hosts generated with the QIAseq xHYB AMR Panel.

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.
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 AMR Panel reference data set is available from QIAGEN Sets Reference Data Library accessible via References (Image referencemanager_16_n_p) in the top Toolbar.

Launching the workflow

The Find QIAseq xHYB AMR Markers (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) | Find QIAseq xHYB AMR Markers (Human host) (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 2.77). Click on Next.
  3. Choose whether batch units should be defined based on organization of the input data, or by provided metadata (figure 2.78). 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 2.79). Click on Next.
  6. Verify or select control genes (figure 2.80). Click on Next.
  7. Specify the trim settings (figure 2.81) and click on Next.
  8. Finally, select a location to save outputs to and click on Finish.

Image find_qiaseq_reference
Figure 2.77: Select reference data set.

Image find_qiaseq_batching
Figure 2.78: Define batch units.

Image find_qiaseq_marker
Figure 2.79: Select the reference marker database

Image find_qiaseq_controlgenes
Figure 2.80: Select control genes.

Image find_qiaseq_trim
Figure 2.81: Trim settings.

Workflow tools and outputs

The Find QIAseq xHYB AMR Markers (Human host) template workflow consists of the following tools. See figure 2.82 for a full overview of the workflow.

Image find_qiaseq_layout
Figure 2.82: Layout of the QIAseq xHYB AMR Markers (Human host) workflow.

The outputs provided by this workflow are: