DNA Sequencing Facility: Illumina Sequencing

CAP Certified / CLIA Registered
CAP Number: 9041679
CLIA Number: 52D2089533

The DNA Sequencing Facility offers all-inclusive next generation sequencing, DNA extraction and SNP genotyping services on a rolling-submission, fee-for-service basis, with the goal of generating high-quality genomic and transcriptomic data.  We work with our UW system and external collaborators to prepare DNA, RNA, ChIP, GBS, metagenomic, exome, and other sequencing libraries, provide robust sequencing data, and help interpret that data to provide meaningful biological information in a time-sensitive manner.

Getting started

To discuss a project or acquire a quote, please contact our NGS team.  To submit samples, please review our submission guidelines and sequencing policies, fill our our sample submission form, and contact us to set up an account and coordinate sample delivery.

New Services

Whole Metagenome Sequencing

Posted prices assume sequencing 20M reads per sample on the NovaSeq S4 flowcell (coming soon).  Lowering coverage will result in a reduction in sequencing costs of ~$5 per million reads.

Sequencing on the HiSeq 2500 increases price per sample by $100 (UW), $118 (external) for a 12 sample submission.

 12 samples, with a target of 20M reads per sample
- Library preparation + sequencing: $155/sample (UW), $195/sample (external)
   - Library preparation, sequencing + Bioinformatics: $230/sample (UW), $310/sample (external)

24 samples, with a target of 20M reads per sample
- Library preparation + sequencing: $135/sample (UW), $164/sample (external)
   - Library preparation, sequencing + Bioinformatics: $210/sample (UW), $279/sample (external)

48 samples, with a target of 20M reads per sample
- Library preparation + sequencing: $127/sample (UW), $152/sample (external)
   - Library preparation, sequencing + Bioinformatics: $202/sample (UW), $267/sample (external)

Bioinformatics provides a report of all identifiable organisms currently in the database: bacteria, fungi, protists, and dsDNA viruses, along with virulence, antibiotic resistance, and other factors.

Note: We suggest using a DNA extraction methods capable of lysing and isolating DNA from all species, incorporating an enzymatic lysis prior to bead beating


  • Sample Preparation Charges

  • NovaSeq Pricing 9-2018

  • Run Charges - MiSeq

  • Run Charges - HiSeq2500 High Throughput (V4)

  • Run Charges - HiSeq2500 Rapid

  • Bioinformatics

Pricing listed above will be effective starting April 1, 2017. 

EXTERNAL RATES: Clients not affiliated with UW Madison or the University of Wisconsin system are charged a 53% 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.

System Overview

Illumina MiSeq:

  • Read Length: 50, 150, 250 or 300 bp; single read or paired end

  • Run time: 6 hrs - 3 days

  • Data generation per lane: 1-25 million fragments sequenced in parallel; 0.5-15 Gbases data output

  • Ideal for: prokaryotic ChIP-seq, smallRNA-seq, small genome resequencing and targeted capture

Illumina HiSeq 2500:

  • Read length: 50, 100, 150 (rapid mode), or 250 (rapid mode) bp, single read or paired end

  • Run time: 3-6 days in standard mode, 1-3 days in rapid mode

  • Data generation per lane: 100-150 million fragments sequenced in parallel; 7.5-35 Gbases data output

  • Ideal for: de novo genome sequencing, large genome resequencing and targeted sequencing; where quick data turnaround is vital

Scheduling and Sample Submission

Please contact nextgen-seq@biotech.wisc.edu for scheduling information. All projects must be discussed with a project manager prior to submitting samples. No projects will be scheduled until samples and sample submission forms have been dropped off to DNA Sequencing personnel in room 1250 Biotech Center.

 Sequencing Submission Guidelines

Policy Statement

Unless otherwise specified, all data and reagents distributed by the University of Wisconsin Biotechnology Center DNA Sequence 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.

Every effort is made to provide our users with data that meets Illumina performance specifications in a timely fashion. Turnaround time for Illumina sequencing is typically 4-6 weeks.  For more information, please review our Illumina Sequencing Policies prior to submitting samples.

Acknowledging UWBC and the DNA Sequencing Facility

A visible measure of a core's impact is made through proper acknowledgement of usage in publications.  To acknowledge our core, please use the following statement: "The author(s) thank the University of Wisconsin Biotechnology Center DNA Sequencing Facility for providing ________ facilities and services”.


Support is available for projects that are run at UWBC facilities, and is provided for a fee by the UWBC Bioinformatics Resource Center.  Terminals and software are available in our computer lab for clients of UWBC facilities who are internal to UW-Madison or the University of Wisconsin System who need to perform further analysis but lack the necessary hardware and software. Information on the quality reports distributed with your data is a available here.