Illumina

The UW-Madison Biotechnology Center is currently open and following the university’s COVID-19 Response regarding campus operations.

We offer two different Illumina sequencing platforms: Miseq and NovaSeq 6000. All systems offer various flow cell types and read lengths to help meet your throughput needs!


Illumina Platforms

  • ILLUMINA MISEQ SYSTEM

        • Single and paired-end sequencing on a single lane
        • Run times vary from 6 hours to 3 days
        • Nano and Micro flowcells available for coverage need

Please see Table 4 for MiSeq Best Use for your project.

Table 1. MiSeq sequencing run lengths and average reads per flow cell.


  • ILLUMINA NOVASEQ 6000

Illumina S4 Flow Cell and NovaSeq 6000 (Courtesy of Illumina, Inc.)

        • High-Throughput
        • Cost Effective
        • Multiple full and single lane flowcell options

Table 2. NovaSeq 6000 sequencing run lengths and average reads per flow cell.

*two day run time, all others are one day 

Table 3. Read lengths available per flow cell type.  


Comparison between Illumina Platforms
Representative of some applications, please inquire with questions

Table 4. Comparison of services that can be run on MiSeq and NovaSeq 6000.


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: nextgen-seq@biotech.wisc.edu


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 nextgen-seq@biotech.wisc.edu 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 nextgen-seq@biotech.wisc.edu

Shipping Submission

Please send the tracking information to:

Next Generation Sequencing: nextgen-seq@biotech.wisc.edu

*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

Illumina Sequencing Guidelines

  • Questions?

Contact us at nextgen-seq@biotech.wisc.edu with any questions.

  • Sample Storage
    • All input DNA submitted after 9/12/19, along with any intermediate and/or derived products (to include undiluted stock libraries), will be stored for 6 months and then disposed of.
    • All customer prepared libraries submitted after 4/23/18 will be stored for 6 months and then disposed of.

MiSeq Pricing (Effective 5/1/21)


NovaSeq Pricing (Effective 5/1/21)


EXTERNAL RATES: Clients not affiliated with UW Madison or the University of Wisconsin system are charged a 55% surcharge for all labor and incidentals provided; prices are as listed above.  This surcharge is subject to change.

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.