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• Introduction
  • The concept of Biomedical Genomics Analysis
  • System requirements
  • Contact information
• Data import and export
  • BGI/MGI Sequencing Import
  • Illumina Custom Reads
• 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 Panel Analysis
  • The Analyze QIAseq Panels guide
    • Import your reads
    • Start a QIAseq panel analysis
    • Upload to QCI Interpret
  • How to create a custom panel 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 ready-to-use workflows
    • Output from the Identify QIAseq DNA Variants workflows
    • Quality Control for the Identify QIAseq DNA Variants workflow
    • Identify QIAseq DNA Somatic and Germline Variants from Tumor Normal Pair (Illumina)
    • Output from the Identify QIAseq DNA Somatic and Germline Variants from Tumor Normal Pair (Illumina) workflow
  • Create QIAseq DNA CNV Control Mapping workflows
    • Output from the Create QIAseq DNA CNV Control Samples workflow
  • The Identify TMB Status ready-to-use workflows
    • Output from the Identify TMB Status workflow
  • The Detect QIAseq MSI Status ready-to-use workflow
    • Output of the Detect QIAseq MSI Status workflow
  • Detect MSI Status with Baseline Creation ready-to-use workflow
  • Targeted DNA tools detailed description
    • Annotate Structural Variants
    • Convert Annotation Track Coordinates
    • Calculate TMB Score
    • Detect MSI Status
    • Extract Reads Matching Primers
    • Generate MSI Baseline
    • Refine Read Mapping
    • Remove and Annotate with Unique Molecular Index
    • Calculate Unique Molecular Index Groups
    • Create UMI Reads from Grouped Reads
    • Create UMI Reads from Reads
    • Remove Ligation Artifacts
    • Trim Primers of Mapped Reads
    • Identify Mispriming Events
    • Annotate Variants with Unique Molecular Index Info
    • Prepare Guidance Variant Track
    • Import Gene-Pseudogene Table
• Targeted RNAscan
  • The Detect QIAseq RNAscan Fusions ready-to-use workflow
    • Output from the Detect QIAseq RNAscan Fusions workflow
  • The Perform QIAseq RNA Fusion XP Analysis ready-to-use workflows
    • Output from the Perform QIAseq RNA Fusion XP Analysis workflow
  • Interpretation of fusion results
  • Targeted RNAscan tools detailed description
    • Detect and Refine Fusion Genes
    • Annotate Fusions with Known Fusion Information
    • QC for RNAscan Panels
    • Annotate RNA Variants
    • Import Known Fusion Information Track
• Immune Repertoire
  • Perform QIAseq Immune Repertoire Analysis ready-to-use workflow
    • Output from the Perform QIAseq Immune Repertoire Analysis workflow
  • QIAseq Immune Repertoire Expert Tools
    • Import VDJtools Clonotypes
    • Immune Repertoire Analysis
    • Compare Immune Repertoires
• Targeted Multimodal
  • Perform QIAseq Multimodal Analysis (Illumina) ready-to-use workflow
    • Output from the Perform QIAseq Multimodal Analysis (Illumina)
  • Perform QIAseq Multimodal Analysis with TMB and MSI (Illumina) ready-to-use 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 ready-to-use workflow
    • Output from the Quantify QIAseq RNA Expression workflow
  • Targeted RNA tools detailed description
    • The Quantify QIAseq RNA tool
• UPX 3'
  • Demultiplex QIAseq UPX 3' reads
  • The Quantify QIAseq UPX 3' ready-to-use workflow
    • Output from the Quantify QIAseq UPX 3' workflow
• Exome
  • Identify QIAseq Exome Germline Variants
    • Output from the Identify QIAseq Exome Germline Variants ready-to-use workflow
  • 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 ready-to-use workflow
• Targeted Methyl
  • The Detect QIAseq Methylation ready-to-use workflow
    • Output from the Detect QIAseq Methylation workflow
  • Targeted Methyl associated tools
    • Finding differentially methylated regions
    • Create Methylation Level Heat Map
• 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
• Ready-to-use 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)
    • Filter Somatic Variants (WGS)
    • Identify Somatic Variants from Tumor Normal Pair (WGS)
    • Identify Variants (WGS)
  • Hereditary Disease (WGS)
    • Filter Causal Variants (WGS-HD)
    • 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 Variants (WGS-HD)
• Whole exome sequencing (WES)
  • General Workflows (WES)
    • Annotate Variants (WES)
    • Annotate Variants with Effect Scores (WES)
    • Identify Known Variants in One Sample (WES)
  • Somatic Cancer (WES)
    • Filter Somatic Variants (WES)
    • Identify Somatic Variants from Tumor Normal Pair (WES)
    • Identify Variants (WES)
    • Identify and Annotate Variants (WES)
  • Hereditary Disease (WES)
    • Filter Causal Variants (WES-HD)
    • 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 Variants (WES-HD)
    • Identify and Annotate Variants (WES-HD)
• Targeted amplicon sequencing (TAS)
  • General Workflows (TAS)
    • Annotate Variants (TAS)
    • Identify Known Variants in One Sample (TAS)
  • Somatic Cancer (TAS)
    • Filter Somatic Variants (TAS)
    • Identify Somatic Variants from Tumor Normal Pair (TAS)
    • Identify Variants (TAS)
    • Identify and Annotate Variants (TAS)
  • Hereditary Disease (TAS)
    • Filter Causal Variants (TAS-HD)
    • 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)
    • Identify Variants (TAS-HD)
    • Identify and Annotate Variants (TAS-HD)
• 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
  • CNV and LOH Detection
    • Region-level CNV track (Region CNVs)
    • Target-level CNV track (Target CNVs)
    • Gene-level annotation track (Gene CNVs)
    • Loss-of-heterozygosity track
    • CNV results report
    • CNV algorithm report
  • Structural Variant Caller
    • Output from the Structural Variant Caller
  • Target Region Coverage Analysis
    • Output from Target Region Coverage Analysis
• Batching workflows
• Legacy tools
  • Detect Fusion Genes
  • Refine Fusion Genes
• Appendices
  • Install and uninstall plugins
    • Installation of plugins
    • Uninstalling plugins
• Bibliography

Summary outputs

1. Summary Report: A cross-sample, combined report. This report summarizes key QC statistics such as read mapping summary and coverage statistics. See the Reports section for a detailed description.

2. Shared_Variants: A track containing variants with >=50% frequency found in one or more samples.

3. Consensus sequences: A folder containing the consensus sequence for each sample.

4. Genome View: A track list containing:
   • The reference SARS-CoV-2 genome MN908947.3
   • The reference SARS-CoV-2 CDS regions
   • Sample coverage graphs
   • The reference SARS-CoV-2 gene regions
   • The Shared_Variants track

   An example is shown in figure 4.6.

   
   Figure 4.6: An example of the Genome View track list created from analysis of seven SARS-CoV-2 samples

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