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• Introduction
  • System requirements
  • Contact information
• Installing and uninstalling Workbench modules
  • Installation of modules
  • Licensing modules
  • Uninstalling modules
• Tools
  • LightSpeed Methods
    • Trimming
    • Readmapping
    • Deduplication
    • Local realigment
    • Germline variant detection
    • Limitations
  • LightSpeed Fastq to Germline Variants
    • LightSpeed Fastq to Germline Variants outputs
  • Report
• Template Workflows
  • Fastq to Annotated Germline Variants
    • Outputs from Fastq to Annotated Germline Variants
  • Fastq to Annotated Germline Variants with Coverage Analysis
    • Outputs from Fastq to Annotated Germline Variants with Coverage Analysis
  • Fastq to CNV Control
    • Outputs from Fastq to CNV Control
• Licensing requirements for the QIAGEN CLC LightSpeed Module
  • Licensing modules on a Workbench
    • Request an evaluation license
    • Download a license using a license order ID
    • Import a license from a file
    • Configure License Server connection
    • Download a static license on a non-networked computer
  • Licensing Server Extensions on a CLC Server
    • Download a static license on a non-networked machine

Limitations

Data

LightSpeed is developed for and has been optimized on Illumina paired-end short read sequencing data. Analysis of other types of sequencing reads may not result in similar processing times or variant calls of an equivalent quality.

Variant detection

The variant detection algorithm in LightSpeed is based on a model expecting diploid genomes. Therefore LightSpeed cannot be expected to accurately detect germline variants in genomes with other ploidies.

Alternate ploidies of sex chromosomes are not considered in the variant detection algorithm.

Reference sequence

LightSpeed considers all chromosomes to be linear. Hence, for read mapping, circular chromosomes are linearized with position 1 starting at the junction of the chromosome. No reads will be mapped accross the junction of circular chromosomes.

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