Target Enrichment with the Flexibility of Major Sequencing Platform Compatibility 

NGS sequencing has been critical to characterizing biological mechanisms and has enabled extensive analyses of genetic variation and function – from targeted sequencing of known genes and variants to sequencing the whole genome for novel discovery.

To accommodate the breadth of applications that have emerged, a variety of sequencers are available in the market to help perform different levels of research. Each platform offers a unique value to the NGS community and has been engineered to offer the best for some particular niche, application, or field. For most library preparation use cases, sequencer compatibility is key to an application and to a particular lab’s specifications. Factors such as cost, availability of panels and assays, necessary turnaround time, and required per run capacity render sequencer compatibility an important decision when considering a library preparation chemistry.  

Recognizing this reality, Paragon Genomics is proud to offer Targeted NGS solutions compatible with major sequencing platforms such as Illumina and Ion Torrent to leverage these advantages. We offer solutions for a wide variety of applications in Precision medicine, Oncology, Infectious diseases, Agrigenomics, and more.

Paragon Genomics CleanPlex® Technology Highlights

CleanPlex® is an ultra-scalable and ultra-sensitive NGS amplicon sequencing technology that breaks the limits of traditional amplicon-based and hybrid capture-based target enrichment technologies by combining superior primer design and innovative library preparation chemistry. 

It is a patented 3-step, 3-hr rapid amplicon-based NGS target enrichment technology that allows researchers and assay developers to discover more with less.

While most amplicon sequencing technologies are compatible with only a single type of sequencer, CleanPlex® chemistry has been specifically designed to be adaptable with both Illumina and Ion Torrent platforms using the same primer pool, without the need to inventory multiple versions of the same panel.

CleanPlex® Technology offers: 

  • Higher target design rate

  • Higher coverage uniformity

  • Higher on-target rate

While requiring: 

  • Less DNA input (single cell sensitvity)

  • Less time and labor

  • Less sequencing resources (potentially half sequencing required)

Benefits of Sequencing Compatibility

  • Easy to set up new assays with sequencers that are already established in a lab: avoid the need to purchase new equipment.
  • Cost savings depending on which sequencer would be the most cost-efficient based on applications, sample volume, throughput, etc.
  • Reduced inventory cost of reagents, one panel for different sequencing platforms.
  • Supply chain doesn’t depend on just one sequencing provider.
  • Avoiding platform-specific biases in read distributions by application need


Illumina vs. Ion Torrent

IlluminaIon Torrent
Advantages-Large range of sequence capacities for targeted and WGS

-Higher accuracy

-Lowest cost per Gb

-Low instrumental and operation cost (especially startup)

-Real-time sequencing, no need for optical equipment

-Short run time 

-Ideal for smaller targeting applications.

Disadvantages-Limit to short read lengths

-Cost of sequencers

-Index hopping

-Requirement of balanced Indexes

-Higher error rates (false positive)

-Intermediate cost per Gb data

-Emulsion PCR & equipment necessary for pre-sequencing.

Ready-to-Use Panels for Different Applications

Check out our variety of Ready-to-Use panels that are adaptable for llumina and Ion Torrent sequencing platforms (as well as for MGI ). We offer the highest level of personalization with white-glove service offering design consultation and engineering for custom panels for your research needs. 

Have specific requests or questions? Schedule a free consultation with our PhD-level expert scientists to learn how our best-in-class amplicon sequencing custom panel design services can help you advance your work.