Amplicon Sequencing


Amplicon sequencing is a next generation sequencing (NGS) technique used to detect low frequency variants, quantify mixed populations, and analysis multiple samples at scale.

We offer various solutions for ultra-deep amplicon sequencing of PCR products to validate and discover variations in specific genomic regions or screen clones. Our amplicon sequencing services employ the latest technologies for custom, in-depth analysis of amplicons ranging from 100 base pairs (bp) to >10,000 bp.

Applications for amplicon sequencing include antibody library screening, natural antibody repertoire profiling, disease genotyping, CRISPR mutation analysis, 16S and 18S amplicon sequencing, screening of molecular clones, and analysis of plasmid stocks.


Amplicon Sequencing

Multiple Solutions to Answer Every Biological Question



50K reads/sample. Available for amplicons 150-500 bp in size.

Custom Short-Read Amplicon Sequencing


Flexible data quantity options. Available for amplicons >100 bp.

Long-Read Amplicon Sequencing

PacBio® Sequel®

Contiguous sequencing of amplicons up to 10 kb.

    Azenta's Recommendation
 Amplicon Size Applications Library Preparation Type Platform Configuration 
100-250 bp
  • SNP Genotyping
  • Genome editing clone verification
  • Somatic/complex variant discovery

Adapter ligation to
full-length products

Illumina 2x150 bp
 250-550 bp
  • Antibody heavy or light chain
  • Hypervariable 16S
Adapter ligation to
full-length products
Illumina 2x250 bp
2x300 bp
  • Somatic variant analysis 
Fragmentation Illumina 2x150 bp
>550 bp
  • Paired antibody heavy and light chains
  • Full length 16S
  • Variant phasing
Adapter ligation to
full-length products
PacBio Sequel
  •  Somatic variant analysis
Fragmentation Illumina 2x150 bp

What is amplicon sequencing?

Amplicon sequencing is a targeted sequencing method that uses polymerase chain reaction (PCR) to selectively amplify specific DNA fragments or genomic regions of interest. Specific primers are designed to flank the target region and the resulting amplicons are then sequenced to determine the nucleotide sequence.


What is the difference between targeted sequencing and amplicon sequencing?

Targeted sequencing and amplicon sequencing both selectively sequence specific regions of the genome, rather than the whole genome. However, the difference between the two methods lies in how the regions of interest are selected and amplified.

Targeted sequencing amplifies through hybridization capture and uses probes or baits complimentary to the target region in order to selectively capture and enrich for specific genomic regions, such as genes, exons, and other functional regions of the genome. Targeted sequencing often offers greater coverage than amplicon sequencing, as the use of hybridization capture can help mitigate biases in the representation of certain genomic regions.

Amplicon sequencing amplifies DNA fragments using PCR. The target regions are defined by PCR primers designed to anneal specific sequences that flank the areas of interest, initiating the amplification process of the targeted DNA fragments. Amplicon sequencing is often more cost-effective than targeted sequencing as it does not involve the use of capture reagents.

NEW Direct Colony to
Whole Plasmid Sequencing



Features & Benefits

Optimized processes- exceed manufacturer’s specifications for data amount and quality
Results in as few as 8 business days depending upon project type
Multiplexing flexibility enables a more cost-effective assay
Latest long-read technologies
Automation reduces sample handling errors and increases reproducibility
Interactive analysis reports and free post-delivery support

Technical Resources

Case Study | Developing an Inclusion and Safety Monitoring Assay for a Cell Therapy Clinical Trial

A biopharma company required a partner for clinical trial support, with an immediate need for development and validation of a biomarker assay using next generation sequencing with a quick turnaround time. Read the case study to learn how this company was able to streamline clinical testing and accelerate the timeline of its phase 1/2 study.

Blog | NGS, PCR, or Sanger Sequencing: An Assay Selection Guide

This selection guide offers practical information about PCR + Sanger, qPCR, and NGS approaches to help you determine which assay best suits your project requirements, along with an interactive assay selection tool to aid your decision making.

Sample Submission Guidelines

Azenta accepts purified and unpurified amplicons, restriction digested material, fragmented DNA, and plasmids. For detailed sample submission requirements please visit our Sample Submission Guidelines.



All customers receive their raw data as FASTQ files. Customizable data analysis packages are available by request.


For information on our NGS platforms as well as recommended configurations of your projects, please visit the NGS Platforms page. Azenta does not guarantee data output or quality for sequencing-only projects.

10x Genomics

How To Order

Email | Phone 1-877-436-3949, Ext. 1