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• Introduction
  • Contact information
  • System requirements
  • Installing modules
    • Licensing modules
    • Uninstalling modules
  • Installing server extensions
    • Licensing server extensions
• Methods and tools
  • Methods
    • Trimming
    • Readmapping
    • Deduplication
    • Local realignment
    • Structural variant detection
    • UMI grouping
    • Primer trimming
    • Germline variant detection
    • Somatic variant detection
    • Tumor normal variant detection
    • Batching
    • 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
    • Calculate TMB Score (LightSpeed)
    • Copy Number Variant Detection (WGS)
      • Copy Number Variant Detection (WGS) outputs
• 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)
    • Fastq to Germline CNV Control
      • Outputs from Fastq to Germline CNV Control
    • Fastq to Somatic CNV Control
      • Outputs from Fastq to Somatic CNV Control
  • 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
    • QIAseq Fastq to Germline CNV Control
      • Outputs from QIAseq Fastq to Germline CNV Control
    • QIAseq Fastq to Somatic CNV Control
      • Outputs from QIAseq Fastq to Somatic CNV Control
  • 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
    • QIAseq Pro Fastq to Germline CNV Control
      • Outputs from QIAseq Pro Fastq to Germline CNV Control
    • QIAseq Pro Fastq to Somatic CNV Control
      • Outputs from QIAseq Pro Fastq to Somatic CNV Control
• Bibliography

Template Workflows

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Subsections

• General Template Workflows
• Template Workflows - QIAseq Targeted DNA
• Template Workflows - QIAseq Targeted DNA Pro

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