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Biomedical Genomics Analysis

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.

Applications and workflows

  • QIAseq Panel analysis. See the complete list of supported QIAseq Panels here.
  • SARS-CoV-2 panel analysis (ARTIC-v3, QIAseq and Ion AmpliSeq)
  • TruSight Oncology 500 (Illumina) panel workflow
  • 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, the workflows are available under Template Workflows in the Toolbox.

QIAseq Panels analysis workflows

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.

Biomedical tools

A collection of biomedical tools is available from the Biomedical Genomics Analysis folder found in the Tools section of the Toolbox. These include:

  • Tools to handle Unique Molecular Indices (UMIs)
  • Tools that are specific to analysis of QIAseq data
  • Utility tools
  • Immune Repertoire Analysis tools
  • Tools for Oncology Score Estimation
  • Tools facilitating upload of analysis results to QCI Interpret
  • Haplotype Calling tools

See the sections below for descriptions of some of the tools.

Figure 2. The Biomedical Genomics Analysis folder in the Toolbox.

Utility tools

The Biomedical Utility Tools folder contains tools that may be generally useful, for example:

Immune Repertoire Analysis tools

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.

Oncology Score Estimation

Tools for calculating TMB, MSI and HRD scores:

  • Calculate TMB Score: Calculates the number of somatic mutations per megabase and provides TMB status.
  • Detect MSI Status: Detects MSI status by comparing the length of microsatellite regions in a sample to a baseline comprised of microsatellite stable (MSS) samples.
  • Calculate HRD Score (beta): Calculates an HRD score from the number of large-scale chromosomal copy number changes.

Seamless upload of analysis results to QCI Interpret

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.

Haplotype Calling (beta)

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.

  • Microhaplotype Caller (beta): Detects genomic variants and annotates them with read-based phasing information.
  • Genotype track: Represents variants at both allele and locus levels. The Genotype track allele table resembles traditional variant tables by displaying individual variants on separate rows. In contrast, the locus table reports all variants for a given locus in a single row and summarizes called alleles in a genotype annotation.

Additional tools

A number of tools are available in other folders in the Toolbox.

In the Resequencing Analysis folder:

In the Epigenomics Analysis folder:

  • 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.
  • Predict Methylation Profile: Estimates the cell type composition of a sample based on differentially methylated cytosines or regions. It is designed for use with the QIAseq Methyl T-Cell Infiltration Panel (MHS-202Z) that distinguishes epithelial, fibroblasts and immune cells, but can also be applied to other data.
  • Create Methylation Database: Creates a methylation database track of two or three pure conditions. The methylation database can be used as an input to Predict Methylation Profile.

QIAGEN GeneRead Panels

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.

Comprehensive collection of template workflows

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.

Reference data provided through the Reference Data manager

We provide matching reference datasets for all template workflows.

Figure 5. Hg38 no alternative reference dataset in the Reference Data Manager.

Latest improvements

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

 

Downloads

Plugin Manual
Online manual Download manual
Plugin Download
Download plugin
Download Biomedical Genomics Analysis (Beta)

Version

Platform support

Download

23.0.0

QIAGEN CLC Genomics Workbench


 [23.0.1, 23.0]

22.2.0

QIAGEN CLC Genomics Workbench


 [22.0.2]

22.0.4

QIAGEN CLC Genomics Workbench


 [22.0.1, 22.0]

21.2.4

QIAGEN CLC Genomics Workbench


 [21.0.6]

21.2.2

QIAGEN CLC Genomics Workbench


 [21.0.5]

21.1.0

QIAGEN CLC Genomics Workbench


 [21.0.4, 21.0.3]

21.0.0

QIAGEN CLC Genomics Workbench


 [21.0.2, 21.0.1, 21.0]

20.2.1

QIAGEN CLC Genomics Workbench


 [20.0.5]

20.2.0

QIAGEN CLC Genomics Workbench


 [20.0.4]

20.0.1

QIAGEN CLC Genomics Workbench


 [20.0.3, 20.0.2]

20.0.0

QIAGEN CLC Genomics Workbench


 [20.0.1, 20.0]

1.2.1

QIAGEN CLC Genomics Workbench


 [12.0.4, 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
Download plugin
Download Biomedical Genomics Analysis Server Plugin (Beta)

Version

Platform support

Download

23.0.0

QIAGEN CLC Genomics Server


 [23.0.1, 23.0]

22.2.0

QIAGEN CLC Genomics Server


 [22.0.2]

22.0.4

QIAGEN CLC Genomics Server


 [22.0.1, 22.0]

21.2.4

QIAGEN CLC Genomics Server


 [21.0.6]

21.2.2

QIAGEN CLC Genomics Server


 [21.0.5]

21.1.0

QIAGEN CLC Genomics Server


 [21.0.4, 21.0.3]