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Biomedical Genomics Analysis 21.1

Released on 24.06.2021

New features and improvements

Upload to QCI Interpret and QCI Interpret Translational

New tools

New importers/exporters

Structural Variant Caller

RNA-seq read type improvements (QIAseq RNA Fusion XP)

SARS-CoV-2 workflow and reference data

Workflow improvements

In the following QIAseq workflows Structural Variant Caller has been configured with target regions to improve speed:

In the following WGS workflows the new setting Ignore broken pairs in Structural Variant Caller has been enabled to improve speed:

Other improvements

Bug fixes

Biomedical Genomics Analysis Plugin 21.0.1

Released on February 3, 2021

Improvements

Bug fixes

Biomedical Genomics Analysis 21.0

Released on January 12, 2021

New features

Detect and Refine Fusion Genes

Detect and Refine Fusion Genes potential fusions in RNA data and then accumulates and evaluates the evidence for each potential fusion.

This tool replaces the Detect Fusion Genes and the Refine Fusion Genes tools, which have been moved to the Legacy section of the Toolbox. We recommend that workflows containing the legacy tools are updated to include Detect and Refine Fusion Genes instead.

The following ready-to-use workflows have been updated to use Detect and Refine Fusion Genes in place of the the two legacy tools, which they used previously:

Identify Mispriming Events

Identify Mispriming Events produces a track of potential mispriming events, i.e. events where reads were amplified from a region of the genome other than the intended target region. Using this track as input to Trim Primers of Mapped Reads, reads originating from mispriming events can be removed from mappings, decreasing the potential for false positive variants to be called in downstream analysis steps. This track can also be used to evaluate the quality of a set of primers.

Improvements

Performance improvements

Improvements to workflows

Other improvements

Bug fixes

Changes

The following tools have been moved to the QIAGEN CLC Genomics Workbench 21.0:

Retirements

Advance Notice

 

Biomedical Genomics Analysis Plugin 20.2.1

Released on February 3, 2021

Improvements

Bug fixes

Biomedical Genomics Analysis Plugin 20.2

Released on November 26, 2020

New Features

New ready-to-use workflows

New workflows are available under the Ready-to-Use Workflows area of the Toolbox:

New tools

Improvements

Reference data bundles

New datasets supporting the new workflows are available under the QIAGEN Sets tab of the Reference Data Manager:

Bug fixes

 

Biomedical Genomics Analysis Plugin 20.1.1

Released on August 13, 2020

Improvements

Bug fixes

 

Biomedical Genomics Analysis Plugin 20.1

Released on June 29, 2020

New Features

New QIAseq ready-to-use workflows

After plugin installation, these new workflows can be found in the CLC Genomics Workbench Toolbox under Ready-to-Use Workflows | QIASeq Panel Analysis | QIASeq Analysis Workflows. They can also be launched using the Analyze QIAseq Panels guide.

These workflows offer some benefits over the workflows provided in the Whole Exome Sequencing folder for trio and germline variant detection, including incorporating read trimming as an initial step in the workflow, and retaining QUAL scores in the variant track produced. In addition, the Identify QIAseq Exome Germline Variants workflow provides the option to detect CNVs. The Create QIAseq Exome CNV Control Mapping can be used to generate control mappings suitable for use when running CNV detection on exome panel data.

These workflows can be launched from under the new Exome tab of the Analyze QIAseq Panels guide.

Other ready-to-use workflows

New tools

Improvements

Extended support for paired reads, including reads generated by duplex TruSight Oncology, Illumina (TSO) UMI protocol

Other QIAseq Panel Analysis workflow improvements

Reference data

Updated data sets are available under the QIAGEN Sets tab of the Reference Data Manager:

Export and upload

Reports

Quantify QIAseq RNA

Fusion gene detection

Calculate TMB Score has been updated to only use exon regions for calculating the TMB score. For this, it requires a track containing the exon regions (typically, an mRNA track).

Bug fixes

Notifications

Tutorials for the Biomedical Genomics Analysis plugin are provided online. They will no longer be available from the Help | Plugin Tutorials menu of the CLC Genomics Workbench. The online tutorials can be reached using the Help | Online Tutorials menu option.

 

Biomedical Genomics Analysis Plugin 20.0.1

Released on March 10, 2020

Bugfixes

Improvements

Fusion gene pipeline improvements

Various other minor improvements

Biomedical Genomics Analysis Plugin 20.0

Released on December 11, 2019

New Features

QIAseq Panel Analysis

New workflows

VCF Export

An additional VCF exporter, VCF (Biomedical), is now available. This new exporter extends the functionality of the standard VCF exporter by supporting the export of Copy Number Variants (CNV) Tracks (Target, Region and Gene) and Refined Fusion Genes (WT) Tracks, in addition to the export of other variant tracks. VCF files from both exporters are compatible with upload to QCI Interpret.

Fusion gene detection

Detect Fusion Genes

Refine Fusion Genes

New tools

Combine Reports

Reports generated by the following tools provided by Biomedical Genomics Analysis 20.0.0 can be used with the new Combine Reports tool of the CLC Genomics Workbench:

Improvements and bugfixes

UPX 3′ Analysis

The Demultiplex tool for UPX 3′ (Demultiplex 3′) reads in the panel guide has been improved:

The Quantify QIAseq UPX 3′ workflow has been updated. The workflow now:

QIAseq Panel Analysis

Detect QIAseq RNAscan Fusions

The Detect QIAseq RNAscan Fusions workflow has been optimized to maintain specificity after improvements to the fusion detection tools. The main changes are:

Trim Primers of Mapped Reads

Ready-to-Use Workflows

miRNA tools

Biomedical Genomics Analysis Plugin 1.2.1

Released on August 15, 2019

Bugfixes

Biomedical Genomics Analysis Plugin 1.2

Released on June 27, 2019

New Features

QIAseq Panel Analysis

QIAseq miRNA Analysis

General changes, bugfixes and improvements

QIAseq TMB/MSI

QIAseq Targeted DNA 

Biomedical Genomics Analysis Plugin 1.1

Released on April 3, 2019

New Features

At the same time as this plugin release, a new reference data set is being released, and is available via the CLC Genomics Workbench Reference Data Manager: hg38 no alternative reference set. This data set includes scaffolds and a virus decoy sequence for improved performance.

General changes, bugfixes and improvements

QIAseq Panel Analysis

Trim Primers of Mapped Reads

Ready-to-Use Workflows

Prepare Guidance Variant Track

The Download Example Data functionality in the Help menu of the Biomedical Genomics Analysis plugin has been fixed.

Biomedical Genomics Analysis Plugin 1.0

First release, November 28, 2018
A CLC Genomics Workbench with the Biomedical Genomics Analysis plugin installed delivers the functionality previously provided by the Biomedical Genomics Workbench, the QIAseq Targeted Panel Analysis plugin and the QIAGEN GeneRead Panel Analysis Plugin.

Similarly, a CLC Genomics Server with the Biomedical Genomics Analysis Server Plugin installed delivers functionality previously provided using a CLC Genomics Server with a Biomedical Genomics Server Extension license, the QIAseq Targeted Panel Analysis Server Plugin and the QIAGEN GeneRead Panel Analysis Server Plugin.

The listing below is of changes to tools and workflows delivered with the Biomedical Genomics Analysis and Biomedical Genomics Analysis Server Plugin relative to the corresponding earlier functionality. Further changes relevant to Workbench- and Server-specific functionality can be found on the Latest Improvements pages for CLC Genomics Workbench 12.0 and CLC Genomics Server 11.0.

The information on those pages reflects the introduction into those products of some tools previously only available in the Biomedical Genomics Workbench and Biomedical-enabled CLC Genomics Servers. Thus some tools listed as new will not be new to users of the earlier Biomedical products.

Searching for with the name of a Biomedical Genomics Workbench 5.x tool in the Launch tool of the CLC Genomics Workbench 12.0 will return the corresponding tool(s) of interest in the new Workbench. Workflow elements within Ready-to-Use Workflows have the same names as used in the equivalent worfklows in Biomedical Genomics Workbench 5.0.1 wherever this was possible.

Changes relative to the functionality of Biomedical Genomics Workbench 5.0.1, QIAGEN GeneRead Panel Analysis 1.12 and QIAseq Targeted Panel Analysis 1.2

General changes and improvements

Changes to Ready-to-Use Workflows

Bug fixes

Retirements

Advanced Notice

Trim Primers of Mapped Single Reads (legacy) and Trim Primers of Mapped Paired End Reads (legacy) will be retired in a future release.