Amplicon sequencing is a highly targeted approach that enables researchers to analyze genetic variation in specific genomic regions. The ultra-deep sequencing of PCR products (amplicons) allows efficient variant identification and characterization. This method uses oligonucleotide probes designed to target and capture regions of interest, followed by next-generation sequencing (NGS).
Amplicon sequencing is useful for the discovery of rare somatic mutations in complex samples (such as tumors mixed with germline DNA). Another common application is sequencing the bacterial 16S rRNA gene across multiple species, a widely used method for phylogeny and taxonomy studies, particularly in diverse metagenomics samples.
Amplicon sequencing allows researchers to sequence targets ranging from a few to hundreds of genes in a single run. This ultra-high multiplexed PCR approach expedites research by assessing multiple genes simultaneously. Libraries can be prepared in as little as 5–7.5 hours and sequenced in 17–32 hours.
Amplicon sequencing enables a wide range of research applications for the discovery, validation, or screening of genetic variants.
Focused power for sequencing thousands of amplicons in a single run.
Illumina sequencing by synthesis (SBS) chemistry is the most widely adopted NGS technology, generating approximately 90% of global sequencing data.*
Illumina offers integrated amplicon sequencing workflows that simplify the entire process, from library preparation to data analysis and biological interpretation.
Click on the below to view products for each workflow step.
Delivers a range of ready-to-use and custom panels for simple, flexible targeted resequencing that provides high-quality data you can trust.Illumina DNA Prep
A fast, integrated workflow for a variety of applications, from human whole-genome sequencing to amplicons, plasmids, and microbes.TruSight Tumor 15
Focused sequencing research panel to assess 15 genes commonly mutated in solid tumors in a single assay, with a simple, rapid workflow.Nextera XT DNA Library Prep Kit
Library preparation for small genomes (bacteria, archaea, viruses), amplicons, and plasmids in less than 90 minutes.
Illumina targeted sequencing panels facilitate clinical cancer research by providing expert-defined gene content plus simple data analysis and reporting options.Library Prep Kit Selector Library Prep Kit Selector
Determine the best kit for your needs based on project type, starting material, and method or application.DesignStudio Assay Design Tool
An easy-to-use online software tool that provides dynamic feedback to optimize probe designs.
Affordable, fast, and accessible sequencing power for targeted or small genome sequencing in any lab.MiniSeq System
Supports a broad range of targeted DNA and RNA applications for examining single genes or entire pathways.MiSeq System
Enables focused applications, from targeted resequencing to metagenomics, small genome sequencing, and more.NextSeq 550 System
Provides the flexible power you need for whole-genome, transcriptome, and targeted resequencing.
The Illumina genomics computing environment for NGS data analysis and management.Local Run Manager
An on-premises software solution for creating sequencing runs, monitoring run status, and analyzing data.DNA Amplicon App
Streamlined analysis of NGS data enriched for particular target sequences using amplicon reads.16S Metagenomics App
Analyzes DNA from amplicon sequencing of prokaryotic 16S small subunit rRNA genes and provides visuals of taxonomic classification.
A genome browser developed by the Broad Institute of MIT and Harvard that displays NGS data for complex variant analysis.BaseSpace Variant Interpreter
Leverages leading annotation databases and a powerful filtering interface, enabling researchers to rapidly identify disease-associated variants.BaseSpace Correlation Engine
A growing library of curated genomic data to support researchers in identifying disease mechanisms, drug targets, and biomarkers.
Access the proven power of Illumina NGS for low-throughput applications with the small and robust MiniSeq System. Study single genes or entire pathways with a sequencing solution that fits your benchtop, your budget, and your workflow.View System
Targeted sequencing enables researchers to focus on select genes or amplicons that have known associations with cancer. Both predesigned and custom panels are available. Learn more about targeted cancer sequencing.
NGS technology can help rapidly identify causative variants associated with rare and inherited genetic disorders. In contrast, traditional methods are often costly and require extensive testing. Learn more about NGS for genetic diseases.
16S ribosomal RNA (rRNA) sequencing is a common amplicon sequencing method used to identify and compare bacteria within a given sample. It can identify strains that might not be found using other methods. Learn more about 16S rRNA sequencing.
Targeted resequencing can uncover genetic variation in animals and plants. These variants may represent beneficial mutations that can help inform breeding decisions, or mutations linked to disease susceptibility. Learn more about plant and animal sequencing.
*Data calculations on file. Illumina, Inc., 2015