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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
- 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)
QCI Interpret integration
- Prepare QCI Interpret Upload
- Upload Prepared QCI Interpret Report
- Upload to QCI Interpret
Haplotype Calling (beta)
- Genotype track
- Microhaplotype Caller (beta)
  - Output from Microhaplotype Caller (beta)
- Convert to Genotype Track (beta)
- Import VCF to Genotype Track (beta)
- Export Genotype VCF (beta)
- Export Genotype CSV (beta)
- Export Marker Genotypes (beta)
General tools
- Annotate RNA Variants
  - Import Known Fusion Information Track
- 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 Samples workflow
- Detect QIAseq MSI Status
  - Output of the Detect QIAseq MSI Status workflow
- Detect MSI Status with Baseline Creation
- Identify QIAseq DNA Variants
- Identify QIAseq DNA Pro Somatic Variants with LOH Detection
  - Output from the Calculate LOH 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 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
- Identify QIAseq Exome Germline Variants
  - Output from the Identify QIAseq Exome Germline Variants template workflow
- Identify QIAseq Hybrid Capture DNA Germline Variants (Illumina)
  - 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 Lib Kit Variants
  - Output from the Identify QIAseq Multimodal DNA Lib Kit Variants workflows
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 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
- Perform QIAseq FastSelect RNA Gene Expression (ODT-RT primer)
  - Output from the Perform QIAseq FastSelect RNA Gene Expression (ODT-RT primer) workflow
- Detect Wells for UPXome
- Demultiplex QIAseq UPXome Reads
  - Running the QIAseq UPXome workflows
- 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
- Perform QIAseq UPXome RNA Gene Expression (ODT-RT primer)
  - Output from the Perform QIAseq UPXome RNA Gene Expression (ODT-RT primer) workflow
- Perform QIAseq Multimodal RNA Lib Kit Analysis
  - Output from the Perform QIAseq Multimodal RNA Lib 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)
- QIAGEN GeneRead Panel Analysis
  - Output from the QIAGEN GeneRead Panel Analysis
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
Appendices
- Install and uninstall plugins
  - Installation of plugins
  - Uninstalling plugins
Bibliography

Getting started

Data import and export

Most import and export of data is done using the tools delivered as part of the CLC Genomics Workbench. This functionality is described in the CLC Genomics Workbench manual:

Prepare raw data

The first thing to do after data import is to check the quality of the sequencing reads and perform the necessary trimming. Note that the CLC Workbench is able to trim automatically read-through adapters, but if you are not sure you have read-through reads, you will need to provide a Trim Adapter List. To learn how to create an adapter trim list, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Trim_adapter_list.html.

A workflow is available for preparing the raw reads in the QIAGEN CLC Genomics Workbench, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Prepare_Raw_Data.html.

Batching workflows

Batch processing refers to running an analysis multiple times, using different inputs for each analysis run. For example, if you have 10 sequence lists and wish to run 10 mapping analyses, one per sequence list, then these 10 analyses could be launched by setting up one batch job. When a job is run in batch mode, parameter settings stay the same for each run. It is just the inputs that are changed.

See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Launching_workflows_individually_in_batches.html for details.

For launching a workflow with more than one input, where the contents of more than one input should change in each batch, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Batching_workflows_with_more_than_one_input_changing_per_run.html.

See Perform QIAseq Multimodal Panel Analysis for an example of how to launch a workflow in batch mode.