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• Introduction
  • Overview of CLC LightSpeed Module
  • Contact information
  • System requirements
  • Installing modules
    • Licensing modules
    • Uninstalling modules
  • Installing server extensions
    • Licensing server extensions
• Methods
  • Trimming
    • Quality trimming
    • Adapter trimming
  • Generating read mappings
    • Readmapping - short reads
      • Indexing
      • Read mapping and read pairs
    • Readmapping - long reads
      • Indexing
      • Read mapping
    • Remove ligation artifacts
    • Deduplication
    • Local realignment
    • UMI grouping
      • Definitions
    • Primer trimming
  • Structural variant detection
  • Variant detection
    • Germline variant detection
    • Somatic variant detection
    • Tumor normal variant detection
    • Filtered variants
    • Variant detection using target regions
    • Phasing
  • Batch processing
  • Compatibility with CLC Genomics Workbench tools
  • Limitations
• Tools
  • LightSpeed Fastq to Germline Variants
    • LightSpeed Fastq to Germline Variants outputs
  • LightSpeed Fastq to Somatic Variants
    • LightSpeed Fastq to Somatic Variants outputs
  • LightSpeed Fastq to Somatic Variants Tumor Normal
    • LightSpeed Fastq to Somatic Variants Tumor Normal outputs
  • Report from LightSpeed Fastq to Variants tools
    • Summary
    • Input read QC
    • Quality trimming
    • Adapter trimming
    • Mapping statistics
    • Deduplication
    • UMI
    • Ligation artifacts
    • Realignment
    • Primer trimming
    • Coverage and target enrichment
  • LightSpeed Long Reads to Germline Variants (beta)
    • LightSpeed Long Reads to Germline Variants (beta) outputs
    • Genotype track
      • Getting started
      • Locus table
      • Allele table
      • Track view
      • Header view
      • Differences between genotype tracks and variant tracks
      • VCF compatibility
      • Genotype track filtering and annotation
  • Report from LightSpeed Long Reads to Germline Variants
    • Summary
    • Input read QC
    • Quality trimming
    • Mapping statistics
    • Phasing statistics
  • Calculate TMB Score (LightSpeed)
  • Copy Number Variant Detection (WGS)
    • Copy Number Variant Detection (WGS) outputs
  • LightSpeed Utility Tools
    • Calculate QIAseq xHYB HRD Score
      • Calculate QIAseq xHYB HRD Score output
    • Convert Genotype Track to Variant Track (beta)
    • Import VCF to Genotype Track (beta)
    • Genotype Track Amino Acid Changes (beta)
  • Prepare Sequencing Data
    • LightSpeed Demultiplex QIAseq Long Reads
      • LightSpeed Demultiplex QIAseq Long Reads outputs
  • Export genotype track to VCF
  • Export genotype track allele table to CSV
• Template Workflows
  • General Template Workflows
    • Fastq to Germline Variants (WGS)
      • Outputs from Fastq to Germline Variants (WGS)
    • Fastq to Germline Variants (WES)
      • Outputs from Fastq to Germline Variants (WES)
    • Fastq to Somatic Variants (WGS)
      • Outputs from Fastq to Somatic Variants (WGS)
    • Fastq to Somatic Variants (WES)
      • Outputs from Fastq to Somatic Variants (WES)
    • Fastq to Somatic Variants (Tumor Normal) (WGS)
      • Outputs from Fastq to Somatic Variants (Tumor Normal) (WGS)
    • Fastq to Somatic Variants (Tumor Normal) (WES)
      • Outputs from Fastq to Somatic Variants (Tumor Normal) (WES)
  • Template Workflows - QIAseq Targeted DNA
    • QIAseq Fastq to Germline Variants
      • Outputs from QIAseq Fastq to Germline Variants
    • QIAseq Fastq to Somatic Variants
      • Outputs from QIAseq Fastq to Somatic Variants
  • Template Workflows - QIAseq Targeted DNA Pro
    • QIAseq Pro Fastq to Germline Variants
      • Outputs from QIAseq Pro Fastq to Germline Variants
    • QIAseq Pro Fastq to Somatic Variants
      • Outputs from QIAseq Pro Fastq to Somatic Variants
  • Template Workflows - QIAseq xHYB
    • QIAseq xHYB CGP FFPE Fastq to Somatic Variants
      • Outputs from QIAseq xHYB CGP FFPE Fastq to Somatic Variants
    • QIAseq xHYB CGP Fastq to Somatic Variants
      • Outputs from QIAseq xHYB CGP Fastq to Somatic Variants
    • QIAseq xHYB CGP cfDNA Fastq to Somatic Variants
      • Outputs from QIAseq xHYB CGP cfDNA Fastq to Somatic Variants
    • Providing alternative CNV controls - QIAseq xHYB
    • QIAseq xHYB HRD FFPE Fastq to Somatic Variants
      • Outputs from QIAseq xHYB HRD FFPE Fastq to Somatic Variants
    • QIAseq xHYB HRD Fastq to Somatic Variants
      • Outputs from QIAseq xHYB HRD Fastq to Somatic Variants
  • Template Workflows - QIAseq xHYB Long Read
    • QIAseq xHYB Long Reads to Germline Variants (ONT) (beta)
      • Outputs from QIAseq xHYB Long Reads to Germline Variants (ONT) (beta)
    • QIAseq xHYB Long Reads to Germline Variants (PacBio) (beta)
      • Outputs from QIAseq xHYB Long Reads to Germline Variants (PacBio) (beta)
    • Guide to changing reference data
  • Template Workflows - Twist
    • Twist CGP Fastq to Somatic Variants
      • Outputs from Twist CGP Fastq to Somatic Variants
    • Providing alternative CNV controls - Twist
    • Twist CGP cfDNA Fastq to Somatic Variants
      • Outputs from Twist CGP cfDNA Fastq to Somatic Variants
• Bibliography

Template Workflows - QIAseq xHYB

The QIAGEN CLC LightSpeed Module comes with a series of template workflows facilitating both somatic and germline variant detection. The workflows are pre-configured to process reads from different protocols. In this chapter, template workflows that are specifically designed to analyse data generated with QIAseq xHYB CGP and QIAseq xHYB HRD panels are described.

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Subsections

• QIAseq xHYB CGP FFPE Fastq to Somatic Variants
• QIAseq xHYB CGP Fastq to Somatic Variants
• QIAseq xHYB CGP cfDNA Fastq to Somatic Variants
• Providing alternative CNV controls - QIAseq xHYB
• QIAseq xHYB HRD FFPE Fastq to Somatic Variants
• QIAseq xHYB HRD Fastq to Somatic Variants

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