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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
- 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 (beta)
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
- 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
- Convert Legacy QIAseq Custom Analyses
QIAseq DNA workflows
- Create QIAseq DNA CNV Control Mapping
  - Output from the Create QIAseq DNA CNV Control Mapping workflow
- Detect QIAseq MSI Status
  - Output of the Detect QIAseq MSI Status workflow
- Detect MSI Status with Baseline Creation
- Identify QIAseq DNA and QIAseq DNA Pro Variants
- Identify QIAseq DNA Pro Somatic Variants with LOH Detection
  - Output from the Calculate LOH workflow
- Identify QIAseq DNA Pro Somatic Variants with MSI (Illumina)
  - Output from the Identify QIAseq DNA Pro Somatic Variants with MSI (Illumina) workflow
- Identify QIAseq DNA Somatic Variants with HRD Score (beta)
  - Output from the Identify HRD Score workflow
- Identify QIAseq DNA Somatic Variants with TMB Score
  - Output from the Identify TMB Status workflow
- Identify QIAseq DNA Ultra Somatic Variants
- Create QIAseq Hybrid Capture CNV Control Mapping (Illumina)
  - Output from the Create QIAseq Hybrid Capture CNV Control Mapping (Illumina)
- Identify QIAseq Hybrid Capture Causal Inherited Variants in Trio
  - Output from the Identify QIAseq Hybrid Capture Causal Inherited Variants in Trio
- Identify QIAseq Hybrid Capture DNA Germline Variants (Illumina)
  - Output from the Identify QIAseq Hybrid Capture DNA Germline Variants (Illumina) workflow
  - Identify QIAseq Hybrid Capture DNA Germline Variants including Mitochondrial (Illumina)
- Identify QIAseq Hybrid Capture DNA Somatic Variants (Illumina)
  - Identify QIAseq Hybrid Capture DNA Somatic Variants including Mitochondrial (Illumina)
- Identify QIAseq Multimodal DNA Library Kit Variants
  - Output from the Identify QIAseq Multimodal DNA Library Kit Variants workflows
  - Create QIAseq Hybrid Capture CNV Control Mapping (with UMI) (Illumina)
- Identify QIAseq Somatic Variants (WGS) (Illumina)
  - Output from the Identify QIAseq Somatic Variants (WGS) (Illumina) template workflow
QIAseq RNA workflows
- Detect QIAseq RNAscan Fusions
  - Output from the Detect QIAseq RNAscan Fusions workflow
- Perform QIAseq RNA Fusion XP Analysis
  - Output from the Perform QIAseq RNA Fusion XP Analysis workflows
- Perform QIAseq FastSelect RNA Analysis
  - Output from the Perform QIAseq FastSelect RNA Analysis workflow
- Detect Wells for UPXome
- Demultiplex QIAseq UPXome Reads
- Perform QIAseq UPXome RNA Analysis
  - Output from the Perform QIAseq UPXome RNA Analysis workflow
- Perform QIAseq Multimodal RNA Library Kit Analysis
  - Output from the Perform QIAseq Multimodal RNA Library Kit Analysis workflows
- QIAseq miRNA Differential Expression
- QIAseq miRNA Quantification
  - QIAseq miRNA Quantification outputs
- Quantify QIAseq RNA Expression
  - Output from the Quantify QIAseq RNA Expression workflow
- Demultiplex QIAseq UPX 3' Reads
- Quantify QIAseq UPX 3'
  - Output from the Quantify QIAseq UPX 3' workflow
Other QIAseq workflows
- Detect QIAseq Methylation
  - Output from the Detect QIAseq Methylation workflow
- Perform QIAseq Immune Repertoire Analysis
  - Output from the Perform QIAseq Immune Repertoire Analysis workflow
- Perform QIAseq Targeted TCR Analysis
  - Output from the Perform QIAseq Targeted TCR Analysis workflow
- Perform QIAseq Multimodal Panel Analysis
  - Output from the Perform QIAseq Multimodal Panel Analysis (Illumina)
  - Running multimodal workflows in batch using metadata
- Perform QIAseq Multimodal Panel Analysis with TMB and MSI
  - Output from the Perform QIAseq Multimodal Panel Analysis with TMB and MSI (Illumina)
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
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)
- 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)
- Differential Expression and Pathway Analysis
  - Output from the Differential Expression and Pathway Analysis workflows
- Annotate Variants (WTS)
- Compare Variants in DNA and RNA
- Identify Candidate Variants and Genes from Tumor Normal Pair
- Identify Variants and Add Expression Values
Legacy workflows
- QIAGEN GeneRead Panel Analysis (legacy)
  - Output from QIAGEN GeneRead Panel Analysis (legacy)
Install and uninstall plugins
- Installation of plugins
- Uninstalling plugins
Bibliography

QIAseq DNA workflows

A series of template workflows supporting analysis of data generated using QIAseq panels and QIAseq library preparation kits are available. The workflows generally call variants, but workflows are also available that have additional functionality, such as calculating TMB or MSI.

All template workflows that include variant calling share a common structure:

For unique molecular index (UMI) protocols, the UMI is removed
Reads are trimmed for low quality nucleotides
Reads are mapped
For UMI protocols, UMI consensus reads are generated
The read mapping is realigned
Variants are called and filtered

The template workflows have been optimized using high quality data, settings may therefore not be appropriate for all protocols.

Template workflows are available for analysis of the following QIAseq panels:

Single primer extension panels with UMIs:
- QIAseq Targeted DNA Panels
- QIAseq Targeted DNA Pro Panels
- QIAseq Targeted DNA Ultra Panels
Hybrid capture panels with or without UMIs:
- QIAseq Human Exome
- QIAseq xHYB Human Panels

In addition, template workflows designed to analyze whole genome sequencing (WGS) data can be used to analyze data from the following QIAseq library preparation kits:

QIAseq FX DNA Library Kit
QIAseq Multimodal DNA/RNA Library Kit
QIAseq Ultralow Input Library Kit

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