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QCI Secondary Analysis

Cloud-based secondary analysis for clinical NGS

Accelerate your NGS secondary analysis with the fastest FASTQ to VCF pipeline in the market

With the increasing demand for speed, flexibility, and cost-efficiency in clinical NGS secondary analysis, diagnostic labs need a simple and seamless way to process more sequencing data without extensive time and resource investment.

Paired with QIAGEN’s new LightSpeed Clinical solution, QCI Secondary Analysis provides the fastest, cheapest and highly accurate pipeline currently available for NGS secondary data analysis.

LightSpeed Clinical Secondary Analysis

QCI Secondary Analysis

Break speed and cost barriers with LightSpeed Clinical

LightSpeed Clinical is a new module for QIAGEN CLC Genomics Workbench Premium that empowers clinical laboratories to perform NGS secondary analysis for germline and somatic applications with high accuracy at unprecedented runtimes.

LightSpeed Clinical processes FASTQ files to produce VCF files containing single nucleotide variants (SNV), insertion–deletion mutation (InDel) and structural variant (SV) calls. The module is deployable using local computers or Amazon Web Services (AWS®) cloud and performs quality and adapter trimming, read mapping, deduplication, local realignment, quality control and variant calling.

Joseph Halstead, QIAGEN LightSpeed

Key features of LightSpeed Clinical

Unrivalled speed

Requires less than 20 minutes to process one WGS sample at 35x coverage:

  • 50x faster compared to BWA-GATK industry standard (20 minutes vs. 1200 minutes)
  • 30% faster than Illumina® DRAGEN®*
  • 24% faster than NVIDIA® Parabricks®*

Download benchmark study here.

Lowest cost per sample

Significantly reduces computing costs, requiring less than $0.40 per WGS sample.

  • 95% reduction in computing costs
  • Illumina® DRAGEN®* averages $7.00 per WGS sample
  • NVIDIA® Parabricks®*averages $3.80 per WGS sample

Download benchmark study here.

Gold standard accuracy

Validation rate for WGS variant calls is extremely high, achieving 99% accuracy for more than 90% of the genome.


Go from raw sequencing data to VCF file in five simple steps; Analysis workflows provided for any panel by any vendor.


Enables speed and accuracy without requiring a central processing unit (CPU) or expensive, specialized hardware.

Instant scalability

Allows instant scalability from workflow optimization to to high-throughput production.

*Numbers taken directly from vendor websites (December 2022).

FASTQ to clinical report workflow

QCI Secondary Analysis with LightSpeed Clinical seamless connects to QCI Interpret for an integrated and automated FASTQ to precision report workflow.

QCI Secondary Analysis

QCI Interpret

Agnostic and scalable cloud-based service for clinical NGS secondary analysis (FASTQ to VCF)

  • Panel- and workflow-agnostic, QCI Secondary Analysis can utilize data from any sequencer.
  • Raw FASTQ sequencing files can be directly uploaded to QCI Secondary Analysis via LightSpeed Clinical or any other analysis software.
  • Select pre-configured analysis pipelines optimized for your lab.
  • QCI Secondary Analysis automates the analysis of multiple sequencing runs simultaneously, generating high-quality variant calls within minutes.
  • Visualize analysis results, such as read pileups, in a genome browser directly from the cloud platform. 
  • Send VCF files directly to QCI Interpret or download the results to send to the interpretation platform of your choice.

Clinical decision support platform for clinical NGS tertiary analysis (VCF to precision report)

  • Panel- and workflow-agnostic, QCI Interpret can utilize somatic and germline data from any sequencer.
  • Upload multiple-sample VCF files for different patients, or multiple single sample VCF files for same patient.
  • QCI Interpret’s automatically filters variants and computes classifications according to ACMG and AMP/ASCO/CAP professional guidelines.
  • Review the evidence, literature, and criteria supporting each classification. Determine reportability status.
  • Generate a final precision report that is patient-specific and includes clinically relevant variants, interpretations, and references specified throughout the assessment process.

Learn more about QCI Interpret here.

LightSpeed Clinical sample workflow

With LightSpeed Clinical you can rapidly process FASTQ files to produce highly accurate VCF files in five simple steps.

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Using LightSpeed Clinical in a pediatric intensive care unit

When children’s lives are at stake, every minute counts. To demonstrate how LightSpeed Clinical can help shorten time-to-result for whole-genome sequencing (WGS) in neonatal screening, a pediatric intensive care unit performed a retrospective analysis of WGS data using LightSpeed Clinical from four trios. All confirmed variants were identified in record time, including interpretation using QIAGEN Clinical Insight Interpret in under 55 minutes.


Application Note

Read a benchmark study evaluating the performance of LightSpeed Clinical with regards to speed, cost, and accuracy.

Video Tutorial

View a short video overview of QCI Secondary Analysis, including features, optimizations and sample workflow.

Software Manual

Take a deep-dive into LightSpeed Clinical with the official product manual, providing step-by-step guidance.

Request a free demo

Let us help you optimize your NGS analysis pipeline. Our clinical services team is here to answer your questions and help you get from FASTQ to final report in less time, for less money.

Related NGS testing solutions

QCI Interpret for Hereditary

Clinical decision support software for germline NGS variant interpretation and reporting.

QCI Interpret for Oncology

Clinical decision support software for somatic NGS variant interpretation and reporting.

QIAseq NGS panels

Out-of-the-box and custom NGS panels enabling digital DNA and RNA sequencing to confidently detect low-frequency variants

Product disclaimer:

LightSpeed Clinical is software module to support NGS secondary analysis. The software is NOT intended as a primary diagnostic tool by physicians or to be used as a substitute for professional healthcare advice. Each laboratory is responsible for ensuring compliance with applicable international, national, and local clinical laboratory regulations and other specific accredidations requirements.