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QIAGEN CLC LightSpeed Module delivers an ultra-fast, end-to-end hereditary NGS FASTQ to VCF pipeline. LightSpeed takes raw FASTQ files generated by paired-end 150 bp sequencing protocols and performs quality trimming, adapter trimming, read mapping, deduplication, local realignment, QC and germline variant calling. LightSpeed achieves all of this in as little as 25 minutes for a human whole genome sequenced to 34x coverage and less than 2 minutes for a human whole exome sequenced to 50x coverage, without any requirements for specialized hardware or distributed computing. Additional benchmarking results and details are available in our QIAGEN CLC LightSpeed Module Application Note.
Lightspeed supports any reference sequence, and provides functionality for masking regions during read mapping and restricting variant calling to target regions. The module is optimized for data from Illumina sequencing machines but can also be used on data produced by machines using similar protocols.
QIAGEN CLC LightSpeed Module contains the LightSpeed ”FASTQ to Germline Variants” tool and provides template workflows that make use of this tool. The LightSpeed tool can output a read mapping, a variant track and a QC report, thereby enabling a thorough assessment of sample and variant qualities. The workflows provide functionality for annotating variants, extended QC, creating copy number controls, copy number variant detection and additional visualization features.
Figure 1. Workflows and tools provided by QIAGEN CLC LightSpeed Module that enable fast and easy WGS and WES data analysis.
Figure 2. Details of the “FASTQ to Annotated Germline Variants” workflow. In this detailed workflow, you can see how the data analysis progresses. You can customize the workflow based on your needs.