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Biomedical Genomics Analysis latest improvements

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.