What’s new in version 3.5

Check out the new features and updates in Biomedical Genomics Workbench, including several new guides designed to help you quickly get started with specific applications.

Get started faster with Biomedical Genomics Workbench

• We have prepared several new short Getting Started Guides, which make it easy to get started with specific applications in Biomedical Genomics Workbench

• Find and start any workflow or tool using the new Quick Launch tool


Detect larger deletions with higher accuracy

• The Local Realignment and the InDel and Structural Variants tools, included in all ready-to-use workflows, have new parameters enabling highly precise detection of deletions larger than 100bp. Workflows need to be customized to make use of the new parameters


Enhance your research with public data by downloading from NCBI’s Sequence Read Archive (SRA)

• Search and download sequencing reads (along with associated metadata) from NCBI’s SRA database into Biomedical Genomics Workbench for re-analysis, comparative analysis, or controls


Use RefSeq gene annotations in all workflows and tools or use your own gene annotations in GFF3 format

• All ready-to-use workflows can be run with NCBI RefSeq gene/transcript annotations instead of Ensembl

• Custom gene/transcript annotations can now be imported from GFF3 formatted files and used in any of the ready-to-use workflows


Improve the accuracy of your RNA-seq results

• Improve the accuracy of isoform and gene quantification with a new option to use an expectation-maximization algorithm, similar to that of RSEM, to distribute ambiguous reads between isoform/genes in the RNA-seq tool

• Use the new 3D PCA view to discover factors underlying expression changes in RNA-seq samples

• View RNA-seq expression values, statistics, and GO annotations together in the new Expression Browser table


More workflow customization options for Assay Development

• Specify the names of the workflow outputs with user and timestamp information

• Let the workflow automatically create subfolders for each sample processed


Get results faster

• Get much improved performance when running workflows as all variant filtering, variant comparison, and variant annotation tools are now able to run on multiple cores

Release history



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