Custom Amplicon

Custom Amplicon

Service Description

Our sequencing specialists can provide a custom amplicon library prep service for those who would like to sequence a specific region of interest on our Illumina platforms. We are here to help you from whatever point you’re starting from; whether that is recommendations for primer design or wanting to use primers from a journal article.

We will start with a project consultation where we will discuss optimization of a PCR reaction to amplify your region of interest and our standard amplicon library prep outlined in the chart below.  As these projects are highly customized, please contact us if you are interested in utilizing this service.

Custom Amplicon Workflow

Access our Interactive Submission Guidelines and get the exact guidance you need to prepare, label, and deliver your samples.


If you can’t find the information you’re looking for, please contact us at

Library Preparation Pricing

MiSeq Pricing

Effective 3/1/23

* Read specifications based on Illumina PhiX control library. Output may vary based on library type.
** 2x300 Shared provides ~20,000-70,000 reads per sample. Due to sample quality and quantity variation, there is no minimum read guarantee.

NovaSeq X Plus Pricing

Effective 8/1/23

* M=million. This is targeted number of reads. Actual read counts may vary ±20% from targeted amounts.
** B=billion. Read specifications based on Illumina PhiX control library. Output may vary based on library type.

Illumina pricing is broken into two components: library preparation and run cost.  Library preparation is charged on a per sample basis and varies by type.  Run charges are based on the length of the sequencing run and whether it is single or paired end.  Prices are subject to change due to increasing reagent costs.

Unless otherwise specified, all data and reagents distributed by the University of Wisconsin Biotechnology Center DNA Sequencing Facility are intended for research purposes only. They are not intended nor certified for diagnostic or clinical use. Clinical services are provided through our collaboration with the UW Collaborative Genomics Core.