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Introduction
- The concept of Biomedical Genomics Analysis
- System requirements
- Contact information
Data import and export
Reference Data Management
- QIAGEN Sets
SARS-CoV-2 workflows
- Identify ARTIC V3 SARS-CoV-2 Low Frequency and Shared Variants (Illumina)
- Identify QIAseq SARS-CoV-2 Low Frequency and Shared Variants (Illumina)
- Identify Ion AmpliSeq SARS-CoV-2 Low Frequency and Shared Variants (Ion Torrent)
- SARS-CoV-2 workflow output
  - Summary outputs
  - Sample specific outputs
QIAseq Sample Analysis
- The Analyze QIAseq Samples guide
- How to create a custom sample analysis workflow
  - Import QIAGEN Primers
- Create a custom Trim adapter list (optional)
- Unique Molecular Indexes (UMIs)
  - UMI group sizes
Targeted DNA
- The Identify QIAseq DNA Variants template workflows
- Create QIAseq DNA CNV Control Mapping workflows
  - Output from the Create QIAseq DNA CNV Control Samples workflow
- The Identify TMB Status template workflows
  - Output from the Identify TMB Status workflow
- The Detect QIAseq MSI Status template workflow
  - Output of the Detect QIAseq MSI Status workflow
- Detect MSI Status with Baseline Creation template workflow
- The Identify QIAseq DNA Ultra Variants template workflow
  - Output from the Identify QIAseq DNA Ultra Variants analysis workflow
- The Calculate LOH template workflow
  - Output from the Calculate LOH workflow
- Targeted DNA tools detailed description
Targeted RNAscan
- The Detect QIAseq RNAscan Fusions template workflow
  - Output from the Detect QIAseq RNAscan Fusions workflow
- The Perform QIAseq RNA Fusion XP Analysis template workflows
  - Output from the Perform QIAseq RNA Fusion XP Analysis workflow
- Interpretation of fusion results
- Targeted RNAscan tools detailed description
Immune Repertoire
- Perform QIAseq Immune Repertoire Analysis template workflow
  - Output from the Perform QIAseq Immune Repertoire Analysis workflow
- Immune Repertoire Expert Tools
Targeted Multimodal
- Perform QIAseq Multimodal Analysis (Illumina) template workflow
  - Output from the Perform QIAseq Multimodal Analysis (Illumina)
- Perform QIAseq Multimodal Analysis with TMB and MSI (Illumina) template workflow
  - Output from the Perform QIAseq Multimodal Analysis with TMB and MSI (Illumina)
- Running the workflows in batch using Metadata
Targeted RNA
- The Quantify QIAseq RNA Expression template workflow
  - Output from the Quantify QIAseq RNA Expression workflow
- Targeted RNA tools detailed description
  - The Quantify QIAseq RNA tool
UPX 3'
- Demultiplex QIAseq UPX 3' reads
- The Quantify QIAseq UPX 3' template workflow
  - Output from the Quantify QIAseq UPX 3' workflow
UPXome
- Detect Wells
- The Quantify QIAseq UPXome template workflow
  - Output from the Quantify QIAseq UPXome workflow
Exome
- Identify QIAseq Exome Germline Variants
  - Output from the Identify QIAseq Exome Germline Variants template workflow
- Identify QIAseq xHYB Germline Variants
  - Identify QIAseq xHYB Germline Variants including Mitochondrial
- Create QIAseq Exome CNV Control Mapping
  - Output from the Create QIAseq Exome CNV Control Mapping workflow
- Identify QIAseq Exome Causal Inherited Variants in Trio
  - Output from the Identify QIAseq Exome Causal Inherited Variants in Trio template workflow
Targeted Methyl
- The Detect QIAseq Methylation template workflows
  - Output from the Detect QIAseq Methylation workflow
- Targeted Methyl associated tools
QCI Interpret Integration
- Upload to QCI Interpret
- Prepare QCI Interpret Upload
- Upload Prepared QCI Interpret Report
QIAseq miRNA Analysis
- QIAseq miRNA Quantification
  - QIAseq miRNA Quantification outputs
  - Naming isomiRs
- QIAseq miRNA Differential Expression
- QIAseq miRNA Expert Tools
  - Create UMI Reads for miRNA
TruSight Oncology 500
- The Perform TSO500 DNA Analysis (Illumina) workflow
  - Output from the Perform TSO500 DNA Analysis
- The Perform TSO500 RNA Analysis (Illumina) workflow
  - Output from the Perform TSO500 RNA Analysis
QIAGEN GeneRead DNA Panel Analysis
- The QIAGEN GeneRead Panel Analysis workflow
  - Output from the QIAGEN GeneRead Panel Analysis
- Trim Primers and their Dimers from Mapping
Template workflows descriptions and guidelines
- General Workflow
- Somatic Cancer
- Hereditary Disease
Getting started
- Import sequencing data
- Prepare Raw Data
Whole genome sequencing (WGS)
- General Workflows (WGS)
  - Annotate Variants (WGS)
  - Identify Known Variants in One Sample (WGS)
- Somatic Cancer (WGS)
- Hereditary Disease (WGS)
  - Filter Causal Variants (WGS-HD)
  - Identify Variants (WGS-HD)
Whole exome sequencing (WES)
- General Workflows (WES)
- Somatic Cancer (WES)
- Hereditary Disease (WES)
Targeted amplicon sequencing (TAS)
- General Workflows (TAS)
  - Annotate Variants (TAS)
  - Identify Known Variants in One Sample (TAS)
- Somatic Cancer (TAS)
- Hereditary Disease (TAS)
Whole Transcriptome Sequencing (WTS)
- 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
General tools
- Create Consensus Sequences from Variants
- Structural Variant Caller
  - Output from the Structural Variant Caller
- Detect Regional Ploidy
  - Output from Detect Regional Ploidy
- Calculate HRD Score (beta)
- Target Region Coverage Analysis
  - Output from Target Region Coverage Analysis
Batching workflows
Legacy tools
- CNV and LOH Detection
Legacy workflows
- 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 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 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)
Appendices
- Install and uninstall plugins
  - Installation of plugins
  - Uninstalling plugins
Bibliography

System requirements

Biomedical Genomics Analysis 22.1 is a plugin for use with CLC Genomics Workbench 22.0.2 or newer. The system requirements for CLC Genomics Workbench are provided at http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=System_requirements.html.

The system requirements of Biomedical Genomics Analysis 22.1 are the same as those for the CLC Genomics Workbench apart from the following:

16 GB RAM required
24 GB RAM recommended
Minimum 100 GB free disk space in the tmp directory
Minimum 90 GB free disk space required in the CLC_References directory of the CLC Workbench if you are not connecting to a CLC Server and using a CLC_References area on that server. The reference data location on a CLC Workbench can be changed from the default location, as described in http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=References_management.html.

For QIAseq analysis the following use cases have specific system requirements:

UPX 3' or UPXome analysis on multiple samples sometimes requires more than 24 GB of RAM.
For full Exome, Multimodal Pan Cancer or TMB analysis, we recommend running on a server. The number of cores significantly affects the runtime.