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Introduction
- The concept of Biomedical Genomics Analysis
- System requirements
- Contact information
Getting started
Reference data management
- QIAGEN Sets
UMI tools
- Remove and Annotate with Unique Molecular Index
- Calculate Unique Molecular Index Groups
- Create UMI Reads from Grouped Reads
  - Consensus nucleotide calculation
- Create UMI Reads from Reads
- Create UMI Reads for miRNA
- UMI group sizes
- Annotate Variants with Unique Molecular Index Info
QIAseq tools
- Import QIAGEN Primers
- Quantify QIAseq RNA
  - Output from Quantify QIAseq RNA
- QC for RNAscan Panels
- Import Known Fusion Information Track
- Annotate Fusions with Known Fusion Information
- Validate QIAseq Read Structure (beta)
  - Output from Validate QIAseq Read Structure (beta)
Biomedical utility tools
- Annotate Structural Variants
- Extract Reads Matching Primers
- Identify Mispriming Events
  - Output from Identify Mispriming Events
- Remove Ligation Artifacts
- Trim Primers of Mapped Reads
- Convert Annotation Track Coordinates
Immune repertoire analysis
- Import/Export VDJtools Clonotypes
- Import Immune Reference Segments
- Immune Repertoire Analysis
  - Output from the Immune Repertoire Analysis tool
- Merge Immune Repertoire
  - Merging of clonotypes
  - Output from the Merge Immune Repertoire tool
- Filter Immune Repertoire
- Compare Immune Repertoires
  - Resolving of clonotypes
  - Output from Compare Immune Repertoires tool
- Clonotypes
- Clonotype Sample Comparison
Oncology score estimation
- Calculate TMB Score
- Detect MSI Status
  - Output from Detect MSI Status
- Generate MSI Baseline
- Calculate HRD Score
  - Output from Calculate HRD Score
  - HRD calculation
IPA and QCI Interpret Upload
- Upload to IPA
  - Upload using the Ingenuity Knowledge Base
  - Error handling
- QCI Interpret Upload
General tools
- Annotate RNA Variants
- Detect Regional Ploidy
  - Output from Detect Regional Ploidy
  - Ploidy state detection
- Import Gene-Pseudogene Table
- Prepare Guidance Variant Track
- Refine Read Mapping
- Structural Variant Caller
  - Output from the Structural Variant Caller
- Targeted Methyl associated tools
- Trim Primers and their Dimers from Mapping
QIAseq Panel Analysis Assistant
- QIAseq custom panels
QIAseq DNA workflows
- Analyze QIAseq DNA and QIAseq DNA Pro
  - Output from Analyze QIAseq DNA
  - Quality Control for Analyze QIAseq DNA
- Analyze QIAseq DNA Ultra Somatic
  - Output from Analyze QIAseq DNA Ultra Somatic
- Analyze QIAseq Hybrid Capture DNA
  - Output from Analyze QIAseq Hybrid Capture DNA
- Analyze QIAseq Hybrid Capture DNA Somatic (with UMI)
  - Output from Analyze QIAseq Hybrid Capture DNA Somatic (with UMI)
  - Compare ID SNP variants across samples
- Analyze QIAseq Hybrid Capture DNA in Trio
  - Output from Analyze QIAseq Hybrid Capture DNA in Trio
- Analyze QIAseq Multimodal DNA Panel
  - Output from Analyze QIAseq Multimodal DNA Panel
- Analyze QIAseq Somatic WGS
  - Output from Analyze QIAseq Somatic WGS
- Analyze QIAseq Multimodal DNA Library Kit Somatic WGS (with UMI)
  - Output from Analyze QIAseq Multimodal DNA Library Kit Somatic WGS (with UMI)
- Simplifying filter cascades
QIAseq RNA workflows
- Analyze QIAseq Multimodal RNA Panel
  - Output from Analyze QIAseq Multimodal RNA Panel
- Analyze QIAseq RNA
  - Output from Analyze QIAseq RNA
- Analyze QIAseq RNAscan
  - Output from Analyze QIAseq RNAscan
- Analyze QIAseq RNA Fusion XP
  - Output from Analyze QIAseq RNA Fusion XP
- Demultiplex QIAseq UPX 3' Reads
- Analyze QIAseq UPX 3' RNA
  - Output from Analyze QIAseq UPX 3' RNA
- Analyze QIAseq Multimodal RNA Library Kit
  - Output from Analyze QIAseq Multimodal RNA Library Kit
- Analyze QIAseq FastSelect and UPXome RNA
  - Output from Analyze QIAseq FastSelect and UPXome RNA
  - Detect Wells for UPXome
- Analyze QIAseq miRNA
  - Output from Analyze QIAseq miRNA
Other QIAseq workflows
- Analyze QIAseq Methyl
  - Output from Analyze QIAseq Methyl
- Analyze QIAseq Immune Repertoire
  - Output from the Analyze QIAseq Immune Repertoire (Illumina) workflow
- Analyze QIAseq Targeted TCR
  - Output from the Analyze QIAseq Targeted TCR (Illumina) workflow
TruSight Oncology 500
- Perform TSO500 DNA Analysis
  - Output from Perform TSO500 DNA Analysis
- Perform TSO500 RNA Analysis
  - Output from Perform TSO500 RNA Analysis
WGS, WES, TAS and WTS template workflow descriptions
- General workflows
- Somatic cancer
- Hereditary disease
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 Variants (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 Variants and Add Expression Values
Comparative analysis
- Analyze Tumor Normal Pair
  - Output from the Analyze Tumor Normal Pair workflow
- Differential Expression Analysis
  - Output from the Differential Expression Analysis workflows
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
Appendix
- QIAseq template workflows consolidation overview
- Install and uninstall plugins
  - Installation of plugins
  - Uninstalling plugins
Bibliography

QIAseq RNA workflows

Subsections