• Manuals

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• Welcome to Biomedical Genomics Workbench
  • Introduction to Biomedical Genomics Workbench
  • Available documentation
  • The material covered by this manual
  • We welcome your comments and suggestions
  • Contact information
    • Contact for the Biomedical Genomics Workbench
    • New program feature request
    • Getting help
• Introduction to user interface, workflows, and tracks
  • The start screen
    • The getting started table
    • Import of example data
  • The user interface
    • The Toolbox
  • Workflows - an overview
  • The track format
    • Track types
    • The Genome Browser
• Ready-to-Use Workflows descriptions and guidelines
  • General Workflow
  • Somatic Cancer
  • Hereditary Disease
• Getting started
  • Reference data
    • The Workbench Reference data location
    • Space requirements
    • Where reference data is downloaded from
    • Download and configure reference data
    • Create a custom Reference Data Set
    • Exporting reference data for use in external applications
    • Troubleshooting reference data downloads
  • Create new folder
  • Import sequencing data
    • How to import data
  • Prepare sequencing data
    • Import adapter trim list
    • How to run the Prepare Overlapping Raw Data ready-to-use workflow
    • How to run the Prepare Raw Data ready-to-use workflow
    • Output from the Prepare Overlapping Raw Data and Prepare Raw Data workflows
    • How to check the output reports
• Whole genome sequencing (WGS)
  • General Workflows (WGS)
    • Annotate Variants (WGS)
    • Identify Known Variants in One Sample (WGS)
  • Somatic Cancer (WGS)
    • Filter Somatic Variants (WGS)
    • Identify Somatic Variants from Tumor Normal Pair (WGS)
    • Identify Variants (WGS)
  • Hereditary Disease (WGS)
    • Filter Causal Variants (WGS-HD)
    • Identify Causal Inherited Variants in Family of Four (WGS)
    • Identify Causal Inherited Variants in Trio (WGS)
    • Identify Rare Disease Causing Mutations in Family of Four (WGS)
    • Identify Rare Disease Causing Mutations in Trio (WGS)
    • Identify Variants (WGS-HD)
• Whole exome sequencing (WES)
  • General Workflows (WES)
    • Annotate Variants (WES)
    • Identify Known Variants in One Sample (WES)
  • Somatic Cancer (WES)
    • Filter Somatic Variants (WES)
    • Identify Somatic Variants from Tumor Normal Pair (WES)
    • Identify Variants (WES)
    • Identify and Annotate Variants (WES)
  • Hereditary Disease (WES)
    • Filter Causal Variants (WES-HD)
    • Identify Causal Inherited Variants in Family of Four (WES)
    • Identify Causal Inherited Variants in Trio (WES)
    • Identify Rare Disease Causing Mutations in Family of Four (WES)
    • Identify Rare Disease Causing Mutations in Trio (WES)
    • Identify Variants (WES-HD)
    • Identify and Annotate Variants (WES-HD)
• Targeted amplicon sequencing (TAS)
  • General Workflows (TAS)
    • Annotate Variants (TAS)
    • Identify Known Variants in One Sample (TAS)
  • Somatic Cancer (TAS)
    • Filter Somatic Variants (TAS)
    • Identify Somatic Variants from Tumor Normal Pair (TAS)
    • Identify Variants (TAS)
    • Identify and Annotate Variants (TAS)
  • Hereditary Disease (TAS)
    • Filter Causal Variants (TAS-HD)
    • Identify Causal Inherited Variants in Family of Four (TAS)
    • Identify Causal Inherited Variants in Trio (TAS)
    • Identify Rare Disease Causing Mutations in Family of Four (TAS)
    • Identify Rare Disease Causing Mutations in Trio (TAS)
    • Identify Variants (TAS-HD)
    • Identify and Annotate Variants (TAS-HD)
• Whole Transcriptome Sequencing (WTS)
  • Analysis of multiple samples
  • Annotate Variants (WTS)
  • Compare variants in DNA and RNA
  • Identify Candidate Variants and Genes from Tumor Normal Pair
  • Identify variants and add expression values
  • Identify and Annotate Differentially Expressed Genes and Pathways
• How to edit application workflows
  • Introduction to customized data analysis
  • How to edit preinstalled workflows
• Plugins
• Appendix
  • Reference data overview
  • Mini dictionary
• Bibliography

Available documentation

The documentation for Biomedical Genomics Workbench can be found here: http://www.qiagenbioinformatics.com/support/manuals/.

Two manuals are available for Biomedical Genomics Workbench:

• The Biomedical Genomics Workbench application based manual. This relatively short manual gives a basic introduction to Biomedical Genomics Workbench, which includes a section on how to get started, as well as describing how to use the different ready-to-use workflows for analysis of different types of sequencing data.
• The Biomedical Genomics Workbench reference manual. This comprehensive manual explains the features and functionalities of the Biomedical Genomics Workbench in detail.

If you would like to use a CLC Server, there are two additional manuals that are relevant:

• The CLC Server administrator manual. This manual is for server administrators and describes how to install and manage CLC Servers.
• CLC Server end user manual. This manual is for the users of the CLC Server. In this manual you can find a description of how to use a CLC Server from a CLC Workbench.

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