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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

Output from the Quantify QIAseq UPX 3' workflow

The following outputs are generated:

Gene expression (): A track with gene expression annotations, including counts and expression values for each gene. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=RNA_Seq_result_handling.html for details.
Sample report (): A report containing essential information from all reports produced by the workflow. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Create_Sample_Report_output.html for details.
QC & Reports folder:
- Merge UMI reads report (): Summarizes the identified UMI groups. See Create UMI Reads from Reads for details.
- Remove and annotate UMI report (): Summarizes the identified UMIs. See Remove and Annotate with Unique Molecular Index for details.
- RNA-Seq report (): Summarizes various mapping statistics and biotypes distributions. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=RNA_Seq_report.html for details.
- Trimming first round, Trimming second round, and Trimming third round reports (): Summarize the performed trimming. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Trim_output.html for details.