Home > Biomedical Genomics Analysis (free plugin)
The Biomedical Genomics Analysis plugin to QIAGEN CLC Genomics Workbench offers tools and workflows for all steps from data preprocessing and quality control through to data analyses, annotation and reporting.
When the plugin is installed, the workflows are available under Template Workflows in the Toolbox.
Template workflows are available for many QIAseq protocols. The workflows can be launched from the Toolbox or 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 1. 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 biomedical tools is available from the Biomedical Genomics Analysis folder found in the Tools section of the Toolbox. These include:
See the sections below for descriptions of some of the tools.
Figure 2. The Biomedical Genomics Analysis folder in the Toolbox.
The Biomedical Utility Tools folder contains tools that may be generally useful, for example:
A collection of tools for performing immune repertoire analysis for T or B cell receptors are provided. Reads are clonotyped by identifying the V, D, J and C segments and annotating the CDR3 region. V, D, J and C reference segments can be imported from IMGT format. The clonotyped reads can be visualized as alignments and Sankey plots.
Tools for calculating TMB, MSI and HRD scores:
The Biomedical Genomics Analysis folder contains tools for uploading a wide range of variants and scores 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.
A collection of tools and a track that support haplotype-aware variant detection and import / export of variants annotated with phasing information from VCF. Phasing can be visualized in a genome browser view, where phased variants are connected by a vertical line.
A number of tools are available in other folders in the Toolbox.
In the Resequencing Analysis folder:
In the Epigenomics Analysis folder:
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.
A wide variety of template workflows are available for specific types of data: whole genome sequencing (WGS), whole exome sequencing (WES) and targeted amplicon sequencing (TAS). General Analysis workflows for identification and annotation of variants, irrespective of disease. Somatic Cancer workflows are 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 3. Template workflows available for analyzing whole genome sequencing data.
Template workflows for whole transcriptome sequencing (WTS) are also provided.
Figure 4. Template workflows for whole transcriptome sequencing.
We provide matching reference datasets for all template workflows.
Figure 5. Hg38 no alternative reference dataset in the Reference Data Manager.
We frequently release updates and improvements such as new features or bug fixes. To get a complete overview, please visit the latest improvements page.