Home > Biomedical Genomics Analysis (free plugin)
The Biomedical Genomics Analysis plugin to QIAGEN CLC Genomics Workbench offers workflows and tools for all steps from the initial data processing and quality control through to data analyses, annotation and reporting.
When the plugin is installed, additional workflows will be accessible from the Toolbox under ‘Template Workflows’.
Figure 1. The available template 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.
Figure 2. The QIAseq Panel Analysis guide interface. The various panel types have their own tabs, and the well picker for demultiplexing UPX 3’ is shown.
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.
A collection of tools for analyzing Immune Repertoire TCR and BCR data from various kits are provided. It is possible to import IMGT reference segments for TCR and BCR and perform downstream filtering and comparison of the clonotype repertoires. Clonotypes can be exported in the VDJ tools format.
A number of additional tools not directly related to the QIAseq panels are provided, as well. The following tools are available from the plugin:
The QIAseq Panel Expert Toolbox contains tools for uploading a wide range of variants to QCI Interpret and QCI Interpret Translational interpretation software, including SNVs, InDels, CNVs, fusions and inversions, as well as TMB and MSI status. In order to use this functionality please contact sales to purchase a license for QCI Interpret.
QIAGEN GeneRead Panels can be analyzed using a template workflow that can identify and annotate variants in Targeted Amplicon Sequencing data generated with catalogue and custom GeneRead DNAseq Gene Panels.
Figure 4. Application workflow available for analyzing GeneRead sequencing data.
The application workflows are specific to the type of data used as input: Whole genome sequencing (WGS), whole exome sequencing, targeted amplicon sequencing and whole transcriptome sequencing. 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).
Figure 5. Application workflows available for analyzing whole genome sequencing data.
In addition, application workflows for whole transcriptome sequencing are provided.
Figure 6. Workflows for whole transcriptome sequencing.
For all template workflows we provide matching reference datasets. The latest improvement is providing the “Hg38 no alternative reference” dataset for analyzing TMB and WGS and WES workflows. The additional scaffolds and virus decoy sequence in this reference dataset improve the variant calling sensitivity and precision.
Figure 7. Hg38 no alternative reference sequence dataset 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.