Government research centers need fast and reliable ways to track pathogens, study mutations, and support public health surveillance. Our targeted amplicon-based NGS panels give your team the power to sequence full viral genomes, monitor respiratory threats, and investigate host susceptibility with accuracy and speed across Illumina and MGI platforms. These solutions support high-throughput programs, emerging variant detection, and large-scale genotyping efforts that drive national and global research initiatives.
Product Highlights
CleanPlex SARS-CoV-2 Kit
This amplicon-based SARS-CoV-2 NGS panel is designed for COVID-19 Coronavirus research and surveillance, enabling complete genome sequencing of the new SARS-CoV-2 virus responsible for the COVID-19 pandemic. This panel is specific for Illumina Sequencing platforms. The other version is available for MGI sequencing platforms. For high throughput labs, we now have up to 2,688 dual-indexed PCR primer combinations (56 x 48 indexes) for pooling up to 2,688 samples onto a single Illumina flowcell.
CleanPlex SARS-CoV-2 FLEX Kit
This amplicon-based SARS-CoV-2 FLEX NGS panel is designed for Coronavirus research and surveillance, enabling complete genome sequencing of the new SARS-CoV-2 virus responsible for the COVID-19 pandemic. The FLEX panel is built upon the original SARS-CoV-2 Panel and contains additional components for more robust and confident variant calling even when the virus mutates over time.
CleanPlex Respiratory Virus Research Kit
This amplicon-based Respiratory Virus Research Panel is designed for the detection, research, and surveillance of key respiratory pathogens, including SARS-CoV-2 (COVID-19), Influenza (Flu A/B), and Respiratory Syncytial Virus (RSV) (A/B). It enables complete genome sequencing of SARS-CoV-2, alongside subtype-level identification for Influenza A/B and RSV A/B through highly sensitive detection of targeted regions.
AgriType® Auto Targeted Library Kit, 1-Pool
The AgriType® Auto Targeted Genotyping by Sequencing Solution is designed and developed to address large-scale agrigenomics projects. The AgriType solution is powered by our advanced primer design algorithm and an efficient ultra-high multiplex PCR-based target enrichment chemistry. AgriType products provide a cost-effective solution for constructing targeted NGS libraries to quickly and efficiently screen hundreds to thousands of markers of interest, thereby accelerating genotyping by sequencing (GBS) studies in fields such as aquaculture, livestock farming, and seed breeding.
NGS Custom Panel
Over 1600 Custom NGS Panels (Next-Generation Sequencing Assays), including both DNA and RNA panels, have been expertly designed and shipped to hundreds of NGS labs globally for research and testing applications ranging from tumor profiling, cancer liquid biopsy, pharmacogenomics, neurology, cardiology, infectious disease, to food safety and agrigenomics.
Examples of Amplicon-Based NGS for Government Research Centers
NGS for Coronavirus
Government research centers rely on fast and reliable ways to study pathogens that affect public health. Paragon Genomics created a highly multiplexed amplicon-based target enrichment panel that covers the full SARS-CoV-2 genome. This panel supports complete genome sequencing and epidemiological research on the virus that caused the COVID-19 pandemic. It moves RNA to sequence-ready libraries in about 5.5 hours. Versions are available for both Illumina and MGI platforms. CleanPlex Technology lets government labs sequence samples with confidence as they track viruses and monitor infectious disease activity. For high-throughput programs, combinatorial dual-indexed PCR primer combinations allow pooling of up to 2,688 samples on a single Illumina flow cell.
NGS for Malaria
Government research teams studying malaria need tools that capture genetic diversity across many samples. Researchers showed that multiplex PCR can sequence 100 heterozygous microhaplotypes and major drug resistance targets in one reaction with deep coverage. They detected minority alleles in Dried Blood Stain samples down to 10 parasites per microliter of blood, performing better than whole genome sequencing that used much higher read counts. This multiplex PCR approach also supports stronger estimates of genetic diversity and relatedness between polyclonal samples when compared with SNP-only panels. These findings position this method as a promising tool for understanding transmission patterns of P. falciparum.
NGS for Ebola Virus
Government labs and health professionals who monitor high-threat pathogens like the Ebola virus rely on sequencing tools that support genomics research across human and viral samples. Scientists at Broad Institute collaborated with Paragon Genomics to design multiple panels for RNA viruses such as Ebola virus using CleanPlex and CleanPlex UMI technologies. The custom assay uses a simple single tube workflow that reduces handling errors and supports work in secure lab settings that depend on advanced genomic technologies.
Researchers used NGS to obtain full viral genomes from clinical samples with low viral content at a rapid and cost-effective pace, allowing teams to accelerate breakthroughs in pathogen tracking. Their analyses of viral genomes and minor variants support studies on disease evolution and viral diversity, and enhance genomic technologies used across government research programs.
Why Choose CleanPlex NGS Sequencing Panels
CleanPlex Ready-To-Use and Custom NGS Panels are powered by Paragon Genomics’ CleanPlex Technology, an ultra-high PCR amplicon-based targeted sequencing technology for NGS.
Government research centers can select from ready-to-use pathogen panels for coronavirus, respiratory viruses, and host susceptibility studies, or request fully custom assays designed around specific genomic targets. Our team builds custom panels in a complete kit format that move nucleic acid samples to sequencing-ready libraries in approximately four weeks.
With CleanPlex NGS Sequencing Panels, you get:
- Fast Turn-Around Time: Accelerate your assay development project. Get your NGS panels in less than 4 weeks (from design acceptance to shipment).
- Cost-Effective Sequencing: Generate data with high on-target performance and coverage uniformity to minimize cost of sequencing.
- Ultra-High Multiplexing: Multiplex up to 20,000+ amplicons per pool for large NGS panels to help you unlock new applications using a faster and simpler workflow.
- Flexible and Scalable Content: Update your custom NGS Panels as you gather new insights.
- High Performance: Jumpstart your work with NGS panels tailored to your needs. Our panels are expertly designed with high first-pass success and high target design rate.
- High Level of Support: Receive fast and comprehensive support throughout the design and ordering process. Our PhD-level expert scientists are here to help.
Here From Our Satisfied Customers
“Cost-effectiveness, accessibility, and usability made Paragon Genomics the right fit. CleanPlex panels helped us streamline our NGS workflow, enabling our team to scale oncology testing with confidence. The uniformity and data quality are excellent, and being able to go from sample to sequencing-ready libraries in under 6 hours is a game-changer.”
Angélica Rodríguez, National Oncology Institute, PanamaI was very impressed by how well the CleanPlex SARS-CoV-2 panel worked when we evaluated it back in March. Working with Paragon Genomics, we were able to leverage the panel to quickly launch a SARS-CoV-2 whole-genome sequencing assay and used it effectively for a number of genomic epidemiology studies.”
Xiaowu Gai, PhD, Director of Bioinformatics, Children's Hospital Los AngelesParagon Genomics has streamlined our workflow, from assay design and optimization to laboratory implementation. Their expertise helped us successfully implement a fully automated process using a custom-designed CleanPlex UMI panel, enabling low variant allele frequency (VAF) detection critical for our projects. Paragon’s excellent bioinformatics services and customer support services were key to achieving our goals.”
Ian Mongrain, Director of Operations, Montreal Heart Institute - Pharmacogenomics CentreWhen we decided to choose a targeted sequencing platform, we had several choices and I am delighted that we chose Paragon Genomics. Paragon Genomics has enabled us to move our sequencing in-house with an affordable and easy-to-use product. They assisted us every step along the way from choosing the amplicons, to guiding us through library preparation to assisting with analysis. I strongly recommend their CleanPlex® amplicon-based targeted sequencing approach and could not be happier with their product.”
Elliot Stieglitz, MD, Associate Professor, University of California San FranciscoWe’re using Paragon’s CleanPlex and CleanPlex UMI technologies to sequence RNA viruses. These technologies enable us to rapidly and cost-effectively obtain complete viral genomes from clinical samples with low viral content. Further analyses of viral genomes, including the identification of minor variants, elucidates viral diversity and evolution. Paragon has enthusiastically worked with us to tackle this new application; they have diligently designed panels to our specifications, meeting with us frequently to optimize the design.”
Aaron Lin, PhD; Erica Normandin; Kim Lagerborg, The Broad Institute of MIT and HarvardParagon Genomics designed a high-quality NGS custom panel for us within two weeks. Its CleanPlex® targeted library technology is fast and easy to use with great PCR uniformity and on-target rate. We are very satisfied by CleanPlex product performance and the superb technical and customer support provided by the Company.”
Chongjian Chen, PhD, CEO, AnnoroadWe are looking for a ‘future proof method’, a better way to do high throughput screening at a species level diagnosis. Paragon Genomics has developed a rapid 2.5-hour library preparation allowing multi-gene methodology, letting us look at lots of unique loci across multiple genomes. It offers a ‘one and done’ approach instead of many different disconnected experiments.”
Scott Geib, PhD, Research Entomologist, USDA-ARS