Short Read Sequencing


Service Description

Our Whole genome sequencing (WGS) service provides a broad overview of the entire genome. This type of sequencing only requires 10ng of input DNA and allows researchers to explore the genome for both small and large variants. WGS can be done on a multitude of organisms such as human, bacteria, fungi, and plants as well as metagenomes. Depending on the sequencing required for the project, WGS libraries can be run on either Illumina’s MiSeq or NovaSeq 6000.

Genome Assembly

Whole genome sequencing can be used for reference based sequencing or assembly, the comparison of new sequencing to a known reference sequencing. Conversely, whole genome sequencing is also ideal for discovering novel genomes because it offers a large amount of data to help characterize/identify any species. We recommend combining long read and short read sequencing to create a comprehensive genome assembly. Check out the Whole Genome Sequencing – Long Read page for more information.

Metagenomic Sequencing

Metagenomic sequencing allows researchers to analyze all microbial genomes present within one sample collection. It allows researchers to study microbial genomes that otherwise can’t be cultivated. This method can be performed using DNA from various types of environmental samples such as air, soil, aquatic sediment, microbiome, city (subways), and marine. If you are interested in specifically targeting the bacteria, fungi, or eukaryotic organisms within an environmental sample, then please check out the 16s/18s/ITS Amplicon Sequencing page

Getting Started

To discuss a project or acquire a quote, please contact us! For new clients, please set up an account (see New Lab or Customer Access below). All projects must be discussed before samples are submitted.

If you would like to initiate a project or get more information, please use the following contact information, and a member of our group will get in touch with you directly.

Next Generation Sequencing:

New Lab or Customer Access

We MUST have this information before we can proceed with your request.

Adding a new lab:

    • Name, address, phone number, UW NetID and email of the Principal Investigator (PI) or Primary scientific contact person.
    • Name, address, phone number, FAX number and email of he financial contact person.
    • Name, UW NetID, phone number and email of all individuals who will be using our service.
    • Payment information: For campus users this should be a direct charge number, e.g. a 144 or 133 prefixed account (please send the whole string of characters). For off campus users you can set up a PO or we can send the financial contact person a bill — your choice. Non-UW system users are charged an additional institutional overhead.

Adding a member to an existing lab:

    • Name of the PI whose lab you are joining.
    • Your name, UW NetID, phone number and email.

Sample Submission

Please contact to arrange all sample submissions. Samples and submission forms must be submitted before a project can be entered into our queue.

Submission Forms and Guidelines

Please check the service page guidelines for specific Submission Forms and Guidelines that need to be included with your samples.

Submitting Samples/ Shipping Instructions

After setting up a customer account, filling out submission form, and reviewing submission guidelines, you can now submit or send samples. *We require customers to submit electronic Submission Forms!*

In Person Submission

Please give advance notice of submission date and time so staff can be prepared to receive samples. Schedule a time for drop off with a staff member at

Shipping Submission

Please send the tracking information to:

Next Generation Sequencing:

*Samples that are being shipped must have a hard copy of the submission form and guidelines in the package! This way we know what the samples are and where they are from.*

If shipping samples from outside UWBC, ship via express shipping carrier on dry ice to the address below:

Next Generation Sequencing
UW DNA Sequencing Facility
Attn: Next Generation Sequencing
425 Henry Mall
1250 Biotechnology
Madison WI, 53706

WGS Short Read Submission Guidelines

Follow the General Guidelines listed (See Above)

-If DNA was quantified using a fluorometric assay (Qubit, Picogreen), please provide 100-500ng of DNA*

-If DNA was quantified using spectrophotometric means (NanoDrop), please provide 500ng-1ug of DNA*

DNA should be clean and free of inhibitors. A good indicator of quality DNA is a NanoDrop reading of 260/280 >1.8 and 260/230 >2.0

Please submit at least 15uL of DNA

*the prep requires 10-100ng input DNA

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.

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.