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For low- to mid-throughput NGS labs

Complete NGS workflows for the Element AVITI System Benchtop Sequencer

Does your lab need an out-of-the-box, simple-to-use, sample-to-report NGS workflow?

For mid-throughput labs with limited IT resources who are interested in using Element’s AVITI™ System benchtop sequencer, QIAGEN provides sample-to-report NGS workflows with panels validated for use on the AVITI System and out-of-the-box downstream data analysis software solutions.

Build your workflow with four NGS steps

Step 1: Library Preparation

QIAseq panels

Step 2: Sequencing by Element

Element AVITI System

Step 3: Cloud-based Data Analysis

QCI Secondary Analysis

Step 4: Interpretation and Reporting

QCI Interpret

Step 1: Library Preparation

QIAseq NGS panels

QIAseq Panels set a new standard for NGS genotyping. Major innovations within this chemistry provide improved ease-of-use, efficiency and expanded variant analysis to simplify and speed-up your NGS workflows.

  • Complete, uniform target coverage – single-tube enrichment for up to 20,000 DNA targets (and an
    additional 8,000 RNA targets for multimodal) staggered placement of primers across the target region
    ensures high uniformity (>99%) and complete coverage.
  • High compatibility with challenging samples – works with FFPE samples, plasma/serum, fresh or frozen
    tissue, cell lines, liquid biopsies with a minimum DNA input requirement as low as 10 ng.
  • Single-day, automation-friendly library preparation – go from sample to sequencing-ready library in 8 hours or less with minimum hands-on time.
  • Customization made easy – boost any cataloged panel with additional content if something is missing or design a custom panel using either our flexible GeneGlobe custom builder or expert design service.
  • Pan-cancer profiling with multimodal approach – comprehensive genomic profiling workflow for simultaneous detection ofDNA variants, RNA fusions and TMB/MSI status in solid tumors and heme malignancies.


Learn more about QIAseq's state-of-the-art enrichment technology

Enables sample to sequencing-ready
libraries in less than 6 hours for detection
of SNVs, small indels, CNVs and loss of
heterozygosity (LOH). Learn more

Curated genome-wide content for a single-day, automation-compatible sample to sequencing workflow that accelerates time to insights. Learn more

Gel-free miRNA Sample to Insight solution for differential expression analysis and novel discovery using next-generation sequencing. Learn more

Step 2: Sequencing

Element AVITI System Sequencing Instrument

The AVITI™ System from Element Biosciences is an out-of-the-box, plug-and-run benchtop sequencer offering an unrivaled combination of performance, cost, and flexibility. Element’s proprietary Avidity Sequencing™ chemistries enable exceptional accuracy and cost efficiency compared to other benchtop systems. With two random access flow cells, the AVITI™ System is equivalent to having two sequencing systems in one.

  • Industry leading accuracy – With > 90% Q30 at 2×150 read length, the AVITI™ System delivers exceptional sequencing accuracy for a comprehensive range of NGS applications.
  • Simple to use – The AVITI™ empowers labs of all sizes and NGS experience with guided workflows, comprehensive run parameters and flexible system settings.
  • Disruptive pricing – Avidity Sequencing technology lowers operating costs with an average of $2-5 per Gb and $0.6-1 per million reads.


Sequence a genome for <$200

Step 3: Cloud-based data analysis

QCI Secondary Analysis with LightSpeed

LightSpeed is a new module for QIAGEN CLC Genomics Workbench Premium that empowers laboratories to perform NGS secondary analysis with high accuracy at unprecedented runtimes. FASTQ files produced from the AVITI™ System are uploaded to LightSpeed. Within minutes (or less), LightSpeed produces 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.

  • Agnostic – Analysis workflows are custom-tailored to panels from any vendor.
  • Ultra-rapid – Requires less than 20 minutes to process one WGS sample at 35x coverage.
  • Cost-efficient – Significantly reduces computing costs, requiring less than $0.40 per WGS sample.


LightSpeed computes 30% faster than Illumina® DRAGEN®

Step 4: Data interpretation and reporting

QCI Interpret

QCI Interpret is an out-of-the-box, fully customizable software solution that enables NGS variant interpretation and reporting for oncology and hereditary applications. VCF files from QCI Secondary Analysis are directly uploaded to QCI Interpret. Users then select a preconfigured workflow, and QCI Interpret automatically filters variants and computes classifications according to ACMG and AMP/ASCO/CAP professional guidelines.

Unlike other tertiary analysis solutions, QCI Interpret uses augmented molecular intelligence (the combination of human and machine curation) to ensure the evidence being considered is accurate, consistent and up-to-date. Users can then review the literature and criteria supporting each variant classification, determine reportability status, and confidently generate a final, patient-specific report with trusted diagnostic, prognostic and therapeutic information.

View a sample report here.


Over 3.5 million NGS patient test cases analyzed and interpreted

Contact us

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