Browse the manual

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
- Validate QIAseq Read Structure (beta)
  - Output from Validate QIAseq Read Structure (beta)
- 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 Somatic Variants template 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' RNA
- Demultiplex QIAseq UPX 3' reads
- The Quantify QIAseq UPX 3' template workflow
  - Output from the Quantify QIAseq UPX 3' workflow
FastSelect RNA
- Perform QIAseq FastSelect RNA Gene Expression (ODT-RT primer)
  - Output from the Perform QIAseq FastSelect RNA Gene Expression (ODT-RT primer) workflow
- Perform QIAseq FastSelect RNA Expression and Fusion Calling (N6-T RT + ODT-RT primer)
  - Output from the Perform QIAseq FastSelect RNA Expression and Fusion Calling (N6-T RT + ODT-RT primer) workflow
- Perform QIAseq FastSelect Rna Expression and Fusion Calling (N6-T RT primer)
  - Output for the Perform QIAseq FastSelect RNA Expression and Fusion Calling (N6-T RT primer) workflow
UPXome RNA
- Detect Wells
- Running the QIAseq UPXome workflows
- The Demultiplex QIAseq UPXome Reads workflow
- Perform QIAseq UPXome RNA Gene Expression (ODT-RT primer)
  - Output from the Perform QIAseq UPXome RNA Gene Expression (ODT-RT primer) workflow
- Perform QIAseq UPXome RNA Expression and Fusion Calling (N6-T RT + ODT-RT primer)
  - Output from the Perform QIAseq UPXome RNA Expression and Fusion Calling (N6-T RT + ODT-RT primer) workflow
- Perform QIAseq UPXome Rna Expression and Fusion Calling (N6-T RT primer)
  - Output for the Perform QIAseq UPXome RNA Expression and Fusion Calling (N6-T RT primer) workflow
Exome and xHYB
- 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
- Identify QIAseq xHYB Somatic Variants
  - Identify QIAseq xHYB Somatic 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

Create QIAseq DNA CNV Control Mapping workflows

Create QIAseq DNA CNV (Pro) Control Mapping template workflows generate mappings suitable for use as baseline, control mappings for the CNV detection step of the Identify QIAseq DNA (Pro) Variants template workflows (see The Identify QIAseq DNA Variants template workflows). We recommend a minimum of 3 control samples be used for creating control mappings.

The Create QIAseq DNA CNV Control Mapping workflows can be found at:

Template Workflows | Biomedical Workflows () | QIAseq Sample Analysis () | QIAseq DNA workflows () | Create QIAseq DNA CNV Control Mapping (Illumina/Ion Torrent) ()

The Create QIAseq DNA Pro CNV Control Mapping workflows can be found at:

Template Workflows | Biomedical Workflows () | QIAseq Sample Analysis () | QIAseq DNA workflows () | Create QIAseq DNA Pro CNV Control Mapping (Illumina/Ion Torrent) ()

These workflows can also be launched from the Analyze QIAseq Samples guide, which is described in The Analyze QIAseq Samples guide. They are available in the drop down menus under each panel analysis listed under either the Targeted DNA or the Targeted DNA Pro tab.

If you are connected to a CLC Server via your Workbench, you will be asked where you would like to run the analysis. We recommend that you run the analysis on a CLC Server when possible.

In the Select reads dialog, specify the sequencing reads to be analyzed.

The following dialog helps you set up the relevant Reference Data Set. If you have not downloaded the Reference Data Set yet, the dialog will suggest the relevant data set and offer the opportunity to download it using the Download to Workbench button.

We recommend that the default QIAseq reference data is selected for use, both when generating control mappings and when analyzing cases using the Identify QIAseq DNA Variants template workflows.

In the next dialog, select the primer track specific to the QIAseq DNA Panel used to generate the sequenced reads. The primer files are specific to the bundles chosen when selecting the reference data.

Note that reads that span the origin of the MT chromosome are not trimmed by the Trim Primers of Mapped Reads tool when running the Identify QIAseq DNA Variants template workflows on data from the DHS-105Z panel.

Subsections

Output from the Create QIAseq DNA CNV Control Samples workflow