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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.
When the plugin is installed, additional workflows will be accessible from the Toolbox under Ready-to-Use Workflows.
Figure 1. The Ready-to-Use Workflows in the Toolbox upon installing the Biomedical Genomics Analysis plugin.
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 UPX 3′ Targeted RNA panel / UPX 3′ Transcriptome Kit. These workflows are located in a separate tab. This solution handles the various multiplexing options of the UPX 3′ kits.
Figure 2. The QIAseq Panel Analysis guide interface.
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.
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.
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 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.
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).
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.