Service Description

16S/18S/ITS (Internal Transcribed Spacers) are three different types of amplicon-based library preparations that allow for cost-effective, high-throughput analysis of microbial environments within a sample collection. We can extract DNA from your environmental samples or prep the DNA that you provide, depending on your project needs. These amplicon-based library preps are typically sequenced on either the Illumina MiSeq or the NovaSeq 6000. Our expert sequencing specialists can help you delve through any microbial diversity research projects and find the best fit for you.

16S/18S/ITS Workflow


Our 16S prep amplifies the V3-V4 hypervariable regions of the 16S rRNA gene in bacteria. For species- and strain-level detection, we offer full-length 16s rRNA amplicon prep and sequencing on our PacBio Sequel II platform – more information about that service can be found here.


18S and ITS sequencing are both used to identify fungal and other eukaryotic organisms within an environmental sample. Our 18S prep amplifies the V9 region of the 18S rRNA gene. Our ITS prep amplifies both the ITS1 and ITS2 regions. Data from the ITS region is advantageous for fungal phylogenetic analysis because this region has more variation than the ribosomal sequences (18S).

Custom and Index PCR 

Not interested in the microbiome, but still want targeted amplicon sequencing? Please check out the index PCR and custom amplicon sequencing services pages for other possibilities.

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 nextgen-seq@biotech.wisc.edu

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.