Sequencing Platform Compatibility
Target Enrichment with the Flexibility of Major Sequencing Platform Compatibility
NGS sequencing has played a major role in characterizing biological mechanisms and enabled deep analysis of genetic variation and function — from targeted gene sequencing of specific variants to whole genome sequencing for novel discovery. Today’s genomic research ranges from sequencing short DNA fragments to running comprehensive genome sequencing workflows across entire populations.
To accommodate this range, researchers rely on different platforms that support everything from targeted panels to full DNA sequencing efforts. A variety of sequencers are available to serve the expanding needs of genomic sequencing — whether you’re focused on specific genes or exploring the genome at scale using flow cell-based generation sequencing technologies. Each system brings unique capabilities to the Next Generation Sequencing (NGS) community, tailored for specific applications or fields of study.
For most library preparation use cases, sequencer compatibility remains a key consideration. Labs weigh factors like cost, panel and assay availability, required turnaround time, and per-run capacity when selecting DNA sequencing platforms. These elements shape the choice of library preparation chemistry and influence overall workflow performance.
Recognizing this, Paragon Genomics offers targeted NGS solutions compatible with major sequencing platforms such as Illumina and Ion Torrent. These solutions support a wide range of research areas, including Precision Medicine, Oncology, Infectious Diseases, and Agrigenomics — all while maximizing the power of modern gene sequencing technologies.
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 sensitivity)
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
Comparing
Illumina vs. Ion Torrent
| Illumina | Ion 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 DNBSEQ™ ). 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.