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University of Wisconsin–Madison

DNA Sequencing Facility

Illumina Sequencing

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.

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 NovaSeq6000:

  • Flow cells: SP (2 lanes, 360M per lane), S1 (2 lanes, 720M per lane), S2 (2 lanes, 1845M per lane), S4 (4 lanes, 2250M per lane)

  • Read length: single end or paired end - 100 cycles (SP, S1, S2), 200 cycles (S1, S2, S4), 300 cycles (SP, S1, S2, S4), 500 cycles (SP only)

  • Run time: 2 days max

  • Data generation per lane: 65GB-3000GB

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

Getting started

To discuss a project or acquire a quote, please contact For new clients, please set up an account.

Sample Submission

Please contact to arrange all sample submissions. Samples and sample submission forms must be dropped off to DNA Sequencing personnel in room 1250 Biotech Center before a project can be entered into our queue. 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. 

Submission Forms and Guidelines

  • Illumina Submission Form (required with every submission) *Please note: Certain elements are not viewable on Mac Preview!


  • Sample Preparation Charges

  • Run charges - NovaSeq

  • Run Charges - MiSeq

  • Bioinformatics

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.

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.