Biomedical Genomics Analysis

The Biomedical Genomics Analysis plugin to the CLC Genomics Workbench offers workflows and tools for all steps from the initial data processing and quality assurance through data analyses, annotation, and reporting.

 

Applications and workflows

  • QIAseq Panel Analysis, including Tumor Mutational Burden (TMB) and Microsatellite Instability (MSI)
  • GeneRead DNAseq Gene Panel Analysis
  • Whole Genome Sequencing (WGS)
  • Whole Exome Sequencing (WES)
  • Targeted Amplicon Sequencing (TAS)
  • Whole Transcriptome Sequencing (WTS)
  • Small RNA Sequencing (miRNA)

When the plugin is installed, additional workflows will be accessible from the Toolbox under Ready-to-Use Workflows.

See the complete list of supported QIAseq panels here.

 

Figure 1. The Ready-to-Use Workflows in the Toolbox upon installing the Biomedical Genomics Analysis plugin.

 

QIAseq Panels analysis workflows

QIAseq Panels analysis workflows for Targeted DNA, Targeted RNAscan and Targeted RNA catalogue and custom panel data can be launched from a dedicated guide interface. The guide provides direct upload of both Illumina and Ion Torrent reads, and the preconfigured workflows can be run using both Illumina and Ion Torrent data. Just click through the tabs to identify the relevant panel and run the workflows directly from the guide. A list of supported QIAseq panels can be found here.

The newest addition to the QIAseq Panel Analysis guide are new workflows for analyzing TMB and MSI. These workflows are located in a separate tab. The TMB workflow must be run in order to get the read mapping input for the MSI workflow. Look in the output reports for the TMB score and MSI status of the sample.

 

Figure 2. The QIAseq Panel Analysis guide interface.

 

 

QIAseq Panel Expert Tools

A collection of QIAseq Panel Expert Tools is installed in the Tools section of the Toolbox. These tools handle Unique Molecular Indices (UMIs) panel data generated by Single Primer Extension (SPE) protocols.

 

Figure 3. The QIAseq Panel Expert Tools in the Toolbox.

 

 

Analyze your QIAseq miRNA reads with Small RNA Analysis workflows

Tools and workflows are now provided for analyzing miRNA reads sequenced using the QIAseq miRNA Kit Library. The tools have been developed to be compatible with CLC Genomics Workbench RNA-Seq tools and are hence located in the RNA-seq Analysis folder.

 

Figure 4. The location of the miRNA tools compatible with the RNA-seq plots and visualization tools.

The output of the analysis can be uploaded directly to Ingenuity Pathway Analysis (IPA) by installing the licensed IPA plugin.

 

 

Functionality for seamless upload of analysis results to QCI Interpret

The QIAseq Panel Expert Toolbox contains a tool for upload of variants and detected fusions to QCI Interpret. This tool allows filtering in relation to genes, regions or variant types before upload. The upload tool can be accessed directly from the QIAseq Panel Analysis guide. In order to use this functionality please contact sales to purchase a license for QCI Interpret.

 

 

QIAGEN GeneRead Panels

QIAGEN GeneRead Panels can be analyzed using a ready-to-use workflow that can identify and annotate variants in Targeted Amplicon Sequencing data generated with catalogue and custom GeneRead DNAseq Gene Panels.

Figure 5. Application workflows available for analyzing whole genome sequencing data.

 

 

Comprehensive collection of Ready-to-Use Workflows

The application workflows are specific to the type of data used as input: Whole Genome Sequencing (WGS), Whole Exome Sequencing (WES), Targeted Amplicon Sequencing (TAS) and Whole Transcriptome Sequencing (WTS). For each of the first three categories, WGS, WES, and TAS, General Analysis workflows can be used for identification and annotation of variants irrespective of disease. Somatic Cancer workflows have been designed specifically for cancer research, including single sample and Tumor-Normal pairs. Hereditary Disease workflows can be used to study variants that cause rare diseases or hereditary diseases (HD) using single sample, Trio and Family of Four study designs.

 

Figure 6. Application workflows available for analyzing whole genome sequencing data.

In addition, application workflows for Whole Transcriptome Sequencing are provided.

Figure 7. Workflows for Whole Transcriptome Sequencing (WTS).

 

 

Reference data provided through the Reference Data manager

For all Ready-to-Use workflows we provide matching reference data sets. The latest improvement is providing the Hg38 no alternative reference data set for analysing TMB and WGS and WES workflows. The additional scaffolds and virus decoy sequence in this reference data set improve the calling of variants and has a positive effect on performance in terms of improved sensitivity and precision.

 

Figure 8. Hg38 no alternative reference sequence data set in the reference data manager.

 

We frequently release updates and improvements such as bug fixes or new features. To get a complete overview, please visit the latest improvements page.

Downloads


Plugin Manual

Download manual

Plugin Download

Download plugin

Download Biomedical Genomics Analysis


Version

Platform support

Download

1.1.0

CLC Genomics Workbench


 [12.0]

Server plugin Downloads

Download plugin

Download Biomedical Genomics Analysis Server Plugin


Version

Platform support

Download

1.1.0

CLC Genomics Server


 [11.0]

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