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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

Coverage and target enrichment

• Average coverage Average coverage calculated across all positions in all target regions. Overlapping paired-read bases are counted only once. Broken read pairs and non-specific read pairs are not included.
• Median coverage Median coverage calculated across all positions in all target regions. Overlapping paired-read bases are counted only once. Broken read pairs and non-specific read pairs are not included.
• Specificity - reads (%) The percentage of mapped read pairs overlapping the target regions. Note that when UMIs are used, this metric is calculated before UMI grouping.
• Specificity - bases (%) The percentage of mapped bases overlapping the target regions. Note that when UMIs are used, this metric is calculated before UMI grouping.
• Specificity - UMI reads (%) The percentage of mapped UMI read pairs overlapping the target regions.
• Specificity - UMI bases (%) The percentage of mapped UMI bases overlapping the target regions.

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