Methods
The CLC LightSpeed Module contains tools which facilitate end to end NGS secondary analysis using an extensive collection of algorithms. Each individual algorithm has been optimized for short runtime with minimal memory requirements while retaining accuracy of variant detection. In the following, the overall principles of core algorithms are described.
Subsections
- 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