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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 and tools
  • Methods
    • Trimming
    • Readmapping - short reads
    • Readmapping - long reads
    • Deduplication
    • Local realignment
    • Structural variant detection
    • UMI grouping
    • Primer trimming
    • Germline variant detection
    • Somatic variant detection
    • Tumor normal variant detection
    • Variant detection using target regions
    • Batch processing
    • Compatibility with CLC Genomics Workbench tools
    • Limitations
  • Tools
    • LightSpeed Fastq to Germline Variants
      • LightSpeed Fastq to Germline Variants outputs
    • LightSpeed Long Reads to Germline Variants
      • LightSpeed Long Reads to Germline Variants (beta)
    • 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
  • 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)
  • Haplotype Calling (beta)
    • Genotype track
      • Genome model
      • Locus table
      • Allele table
      • Header view
      • Track view
    • 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)
• Bibliography

System requirements

In addition to meeting the system requirements of the CLC Genomics Workbench or the CLC Genomics Server, the following requirements must be met:

• All LightSpeed analyses require 32 GB RAM.
• A CPU that supports AVX2 or NEON instruction sets is required.

Compatibility

CLC LightSpeed Module 25.2.1 and CLC LightSpeed Server Extension 25.2.1 can be installed on CLC Genomics Workbench 25.0 and CLC Genomics Server 25.0, respectively, and on later versions in the same major release line.

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