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Biomedical Genomics Analysis

The Biomedical Genomics Analysis plugin to the QIAGEN 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), microsatellite instability (MSI), FLT3 complex variant detection, CNV control sample mapping, UPX 3′ Targeted RNA Panel, UPX 3′ Transcriptome Kit, Multimodal and Fusion XP Panels and QIAseq Whole Exome Panels. See the complete list of supported QIAseq panels here.
  • 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.

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 Multimodal panel as well as picker for barcode demultiplexing for UPX 3′ Targeted RNA panel / UPX 3′ Transcriptome Kit.

 

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.

 

 

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.

 

General tools

A number of additional tools not directly related to the QIAseq panels are provided, as well. The following tools are available from the plugin:

  • Create Methylation Level Heat Map Hierarchically clusters samples and features, generating a two-dimensional heat map of methylation levels, using methylation level tracks as input.
  • Merge Variant Tracks Merges multiple variant tracks into a single variant track.
  • Annotate with Repeat and Homopolymer Information Annotates variants with repeat and homopolymer information, based on the variant itself and the genome sequence flanking it.
  • Annotate with Effect Scores Annotates SNV variants with precomputed effect scores, which indicate the level of impact a mutation has on the gene or transcript.
  • Extract IsomiR Counts Extracts IsomiR composition and count information from each underlying miRNA alignment of the “grouped on mature” expression table output by the Quantify miRNA tool, and produces a table containing that information.
  • Convert Annotation Track Coordinates Converts annotation coordinates, either from hg19 coordinates to hg38 coordinates, or vice versa, making use of the NCBI Remapping Service.
  • Annotate Structural Variants Estimates count, coverage and frequency information for indels detected by the InDels and Structural Variants tool and generates a variant track containing the original variants with these annotations added.

Analyze your QIAseq miRNA reads with Small RNA Analysis workflows

Tools and workflows are provided for analyzing miRNA reads sequenced using the QIAseq miRNA Kit Library. The tools are located in the RNA-seq Analysis folder.

 

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 4. 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 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 (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 7. Hg38 no alternative reference sequence data set in the reference data manager.

VCF export

A new VCF exporter, VCF (Biomedical), is now available. This exporter extends the functionality of the standard VCF exporter by supporting the export of Copy Number Variants (CNV), Refined Fusion Genes and variants tracks in a single CVF file. VCF files from both exporters are compatible with upload to QCI Interpret.

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
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Plugin Download
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Download Biomedical Genomics Analysis

Version

Platform support

Download

20.0.1

QIAGEN CLC Genomics Workbench


 [20.0.2]

20.0.0

QIAGEN CLC Genomics Workbench


 [20.0.1, 20.0]

1.2.1

QIAGEN CLC Genomics Workbench


 [12.0.3]

1.2.0

QIAGEN CLC Genomics Workbench


 [12.0.2, 12.0.1]

1.1.0

QIAGEN CLC Genomics Workbench


 [12.0]
Server Plugin Download
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Download Biomedical Genomics Analysis Server Plugin

Version

Platform support

Download

20.0.1

QIAGEN CLC Genomics Server


 [20.0.2]

20.0.0

QIAGEN CLC Genomics Server


 [20.0.1, 20.0]

1.2.1

QIAGEN CLC Genomics Server


 [11.0.3]

1.2.0

QIAGEN CLC Genomics Server


 [11.0.2, 11.0.1]

1.1.0

QIAGEN CLC Genomics Server


 [11.0]

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