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QCI Secondary Analysis

Scalable, cloud-based service for NGS secondary analysis

powered by DNAnexus®

Analyze with Precision. Interpret with Confidence.


Helping you do more with less

As the rate and volume of raw NGS data generation increases, secondary analysis is becoming a significant bottleneck. The amount of computing power, storage space, security and regulatory compliance, and bioinformatics skill and resources required to keep secondary analysis on pace with sequencing demand is compounding. Today, the goal for many labs is to do more with less.

QCI Secondary Analysis

QCI Secondary Analysis is a new cloud-based service for NGS secondary analysis powered by DNAnexus—the world’s most secure, trusted platform for biomedical data analysis. 

Scalable and workflow agnostic, QCI Secondary Analysis can be used with any NGS instrument and panel combination and seamlessly connects to QCI Interpret, QIAGEN’s platform for clinical NGS interpretation, to enable users to go from FASTQ to precision report through an integrated and automated workflow.

On-demand Webinar
DNAnexus and QIAGEN present an ultra-fast workflow from FASTQ to final report


The DNAnexus difference 

The DNAnexus platform removes bottlenecks in secondary analysis by providing a cloud-based approach that minimizes the need for expensive hardware, additional IT resources, regulatory compliance management, and the development of advanced bioinformatics skills.  Users instead rely on DNAnexus to address the administrative burden of maintaining IT infrastructure, compliance, and quality testing.

• ISO27001
• NIST 800

Why QCI Secondary Analysis

Unparalleled Efficiency

Reduce time and effort with a unified, workflow-agnostic platform that lets you create, refine, validate, and execute pipelines with unprecedented speed.

Unlimited Growth

Scale your environment to meet demand for increased volume with exceptional uptime, powerful compute capacity, and minimal infrastructure investment.

Unrivalled Security

Simplify compliance management and protect data with industry-leading, region-specific security and compliance that evolves overtime to meet requirements.

An integrated workflow from FASTQ to precision report

Panel- and workflow-agnostic, QCI Secondary Analysis can utilize data from any sequencer.

For labs using an Illumina® sequencer and Illumina BaseSpace®, raw FASTQ sequencing files can be directly uploaded to QCI Secondary Analysis. For labs using other sequencers, a bulk file uploader tool can be used to upload data to QCI Secondary Analysis.

Once data has been uploaded to QCI Secondary Analysis, users then select a pre-configured analysis pipeline that has been optimized for their lab’s specific panel, policies, and standard operating procedures (SOPs).  Users also have the option to run and deploy any bioinformatics tools, such as QIAGEN’s CLC Genomics Workbench, within QCI Secondary Analysis.

QCI Secondary Analysis automates the analysis of multiple sequencing runs simultaneously, generating high-quality variant calls within minutes. Users can then visualize the analysis results, such as read pileups, in a genome browser directly from the cloud platform. Or, users can send VCF files directly to QCI Interpret, or download the results to send to the interpretation platform of their choice.

QCI Secondary Analysis seamlessly integrates with QCI Interpret, QIAGEN’s platform for NGS variant interpretation and reporting, via QCI Connect, a secure, cloud-based application. This enables users to go from FASTQ to a precision NGS report through an automated and streamlined workflow to further accelerate turnaround times.

Video Tutorial: QCI Secondary Analysis

Analyze an entire sequencing run in 5 simple steps

Highly flexible and efficient, QCI Secondary Analysis requires minimal resources and expertise to automate and rapidly analyzes an entire sequencing run with very limited hands-on time.

Upload raw sequencing data to QCI Secondary Analysis either through a bulk uploader tool or directly from Illumina BaseSpace®.

Select a pre-configured workflow optimized for your lab’s specific panel, policies, and SOPs.

Click “Start Analysis” and run sequencing data individually or in bulk. An email alert notifies you once the analysis is complete.

Visualize analysis results by sending BAM files directly to genome browsers accessible via the cloud-based platform.

Send VCF files directly to QCI Interpret for downstream interpretation and reporting. Or download the files to local storage and send to the interpretation platform of your choice through LIMS integration.

Request a free demo

Experience the power, flexibility, and simplicity of QCI Secondary Analysis for yourself. Schedule a free, personalized demonstration today.

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