Index PCR

Index PCR

Service Description

Our index PCR service supplements customer amplified products with an Illumina TruSeq adapter. With a modification to the 5′ end of your template specific primers, the amplicons you generate can be purified and submitted to us! We use the amplicons you provide as template in a PCR to add unique indexes and the remainder of the Illumina TruSeq adapter. We then quantify the resulting libraries and pool, QC, and dilute the pooled libraries in preparation for sequencing on Illumina MiSeq or NovaSeq.

Use the file below to confidently add the appropriate sequence to your oligos and order from your preferred vendor. Please consult with if this if your first time using our service.

Concatenation Tool: Illumina Adapter and Region Specific Primer

Custom Amplicon Workflow


This service is ideal for customers who are looking for a cost-effective way to sequence their region of interest and are comfortable performing the initial PCR reactions.

Clients who would like to use this service must ensure that their products contain the necessary portion of the Illumina TruSeq Universal Adapter Sequence.


Our submission form has a tab to concatenate sequences with your region-specific primers to ensure that the correct primers are ordered for the initial PCR; utilizing these primers is critical to the success of the index PCR reaction we perform. We highly recommend customers order primers that are HPLC purified.

To keep costs low, we do not perform upfront QC prior to index PCR; therefore, you are responsible of ensuring that the initial amplification was efficient, and the final product is clean. Please contact us with any questions and see the guidelines tab for the specifics of the submission process.

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.