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Introduction
- The concept of Biomedical Genomics Analysis
- System requirements
- Contact information
Data import and export
Reference Data Management
- The Reference Data Manager
- QIAGEN Sets
SARS-CoV-2 workflows
- Identify QIAseq SARS-CoV-2 Low Frequency and Shared Variants (Illumina)
- Identify Ion AmpliSeq SARS-CoV-2 Low Frequency and Shared Variants (Ion Torrent)
- SARS-CoV-2 workflow output
  - Summary outputs
  - Sample specific outputs
QIAseq Panel Analysis
- The Analyze QIAseq Panels guide
- How to create a custom panel analysis workflow
  - Import QIAGEN Primers
- Create a custom Trim adapter list (optional)
Targeted DNA
- The Identify QIAseq DNA Variants ready-to-use workflows
- Create QIAseq DNA CNV Control Mapping workflows
  - Output from the Create QIAseq DNA CNV Control Samples workflow
- The Identify TMB Status ready-to-use workflows
  - Output from the Identify TMB Status workflow
- The Detect QIAseq MSI Status ready-to-use workflow
  - Output of the Detect QIAseq MSI Status workflow
- Detect MSI Status with Baseline Creation ready-to-use workflow
- Targeted DNA tools detailed description
Targeted RNAscan
- The Detect QIAseq RNAscan Fusions ready-to-use workflow
  - Output from the Detect QIAseq RNAscan Fusions workflow
- The Perform QIAseq RNA Fusion XP Analysis ready-to-use workflow
  - Output from the Perform QIAseq RNA Fusion XP Analysis workflow
- Interpretation of fusion results
- Targeted RNAscan tools detailed description
Immune Repertoire
- Perform QIAseq Immune Repertoire Analysis ready-to-use workflow
  - Output from the Perform QIAseq Immune Repertoire Analysis workflow
- QIAseq Immune Repertoire Expert Tools
  - Immune Repertoire Analysis
  - Compare Immune Repertoires
Targeted Multimodal
- Perform QIAseq Multimodal Analysis (Illumina) ready-to-use workflow
  - Output from the Perform QIAseq Multimodal Analysis (Illumina)
- Perform QIAseq Multimodal Analysis with TMB and MSI (Illumina) ready-to-use workflow
  - Output from the Perform QIAseq Multimodal Analysis with TMB and MSI (Illumina)
- Running the workflows in batch using Metadata
Targeted RNA
- The Quantify QIAseq RNA Expression ready-to-use workflow
  - Output from the Quantify QIAseq RNA Expression workflow
- Targeted RNA tools detailed description
  - The Quantify QIAseq RNA tool
UPX 3'
- Demultiplex QIAseq UPX 3' reads
- The Quantify QIAseq UPX 3' ready-to-use workflow
  - Output from the Quantify QIAseq UPX 3' workflow
Exome
- Identify QIAseq Exome Germline Variants
  - Output from the Identify QIAseq Exome Germline Variants ready-to-use workflow
- Create QIAseq Exome CNV Control Mapping
  - Output from the Create QIAseq Exome CNV Control Mapping workflow
- Identify QIAseq Exome Causal Inherited Variants in Trio
  - Output from the Identify QIAseq Exome Causal Inherited Variants in Trio ready-to-use workflow
Targeted Methyl
- The Detect QIAseq Methylation ready-to-use workflow
  - Output from the Detect QIAseq Methylation workflow
- Targeted Methyl associated tools
  - Finding differentially methylated regions
  - Create Methylation Level Heat Map
QCI Interpret Integration
- Configuration of the Upload to QCI Interpret tool
- The Upload to QCI Interpret tool
QIAseq miRNA Analysis
- QIAseq miRNA Quantification
  - QIAseq miRNA Quantification outputs
  - Naming isomiRs
- QIAseq miRNA Differential Expression
- QIAseq miRNA Expert Tools
  - Create UMI Reads for miRNA
  - Extract IsomiR Counts
TruSight Oncology 500
- The Perform TSO500 DNA Analysis (Illumina) workflow
  - Output from the Perform TSO500 DNA Analysis
- The Perform TSO500 RNA Analysis (Illumina) workflow
  - Output from the Perform TSO500 RNA Analysis
QIAGEN GeneRead DNA Panel Analysis
- The QIAGEN GeneRead Panel Analysis workflow
  - Output from the QIAGEN GeneRead Panel Analysis
- Trim Primers and their Dimers from Mapping
Ready-to-use workflows descriptions and guidelines
- General Workflow
- Somatic Cancer
- Hereditary Disease
Getting started
- Import sequencing data
- Prepare Raw Data
Whole genome sequencing (WGS)
- General Workflows (WGS)
  - Annotate Variants (WGS)
  - Identify Known Variants in One Sample (WGS)
- Somatic Cancer (WGS)
- Hereditary Disease (WGS)
Whole exome sequencing (WES)
- General Workflows (WES)
- Somatic Cancer (WES)
- Hereditary Disease (WES)
Targeted amplicon sequencing (TAS)
- General Workflows (TAS)
  - Annotate Variants (TAS)
  - Identify Known Variants in One Sample (TAS)
- Somatic Cancer (TAS)
- Hereditary Disease (TAS)
Whole Transcriptome Sequencing (WTS)
- Annotate Variants (WTS)
- Compare Variants in DNA and RNA
- Identify Candidate Variants and Genes from Tumor Normal Pair
- Identify Variants and Add Expression Values
- Identify and Annotate Differentially Expressed Genes and Pathways
General tools
- Merge Variant Tracks
- Annotate with Effect Scores
- Annotate with Repeat and Homopolymer Information
- CNV and LOH Detection
- Structural Variant Caller
  - Output from the Structural Variant Caller
- Target Region Coverage Analysis
Batching workflows
Appendices
- Legacy tools
  - Trim Primers of Mapped Single Reads
  - Trim Primers of Mapped Paired End Reads
- Install and uninstall plugins
  - Installation of plugins
  - Uninstalling plugins
Bibliography

Installation of plugins

Note: In order to install plugins and modules, the CLC Workbench must be run in administrator mode. On Windows, you can do this by right-clicking the program shortcut and choosing "Run as Administrator". On Linux and Mac, it means you must launch the program such that it is run by an administrative user.

Plugins and modules are installed and uninstalled using the Workbench Plugin Manager. To open the Plugin Manager go to:

Help in the Menu Bar | Plugins... () or click on Plugins () in the Toolbar

The Plugin Manager has two tabs at the top:

Manage Plugins. This is an overview of plugins and modules that are installed.
Download Plugins. This is an overview of the plugins and modules available to download and install.

To install a plugin, click the Download Plugins tab. This will display an overview of the plugins that are available for download and installation (see figure 27.1).

Image plug-indialogfirst
Figure 27.1: The plugins and modules that are available for download.

Select an item in the list to display additional information about it on the right side of the dialog. Click on the Download and Install button to install the selected plugin or module.

Accepting the license agreement

The End User License Agreement (EULA) must be read and accepted as part of the installation process. Please read the EULA text carefully, and if you agree to it, check the box next to the text I accept these terms. If further information is requested from you, please fill this in before clicking on the Finish button.

Installing a cpa file

If you have a .cpa installer file for Biomedical Genomics Analysis downloaded to your computer, you can install it by clicking the Install from File button at the bottom of the dialog and specifying the .cpa file.

If you are working on a system not connected to the internet, plugin and module .cpa files can be downloaded from https://digitalinsights.qiagen.com/products-overview/plugins/using a networked machine, and then transferred to the non-networked machine for installation.

Restart to complete the installation

When you close Plugin Manager, a dialog will appear offering the opportunity to restart the CLC Workbench. Newly installed plugins and modules will be available for use after restarting.