NovaSeq 6000 Sequencing


The NovaSeq 6000 is the latest production-scale sequencer from Illumina generating unprecedented output in less than two days. The main technical advancements include:

  • Patterned flow cells with scalable throughputs to accommodate most projects
  • 2-channel chemistry for faster sequencing
  • Reduced imaging and data processing time

The patterned flow cells have a defined, organized array of etched wells that each contain a DNA probe for adhering complementary sequences added to DNA libraries. This patterned flow cell replaces the randomly scattered clusters found in imaging intensive, non-patterned flow cells responsible for slower processing time.

The instrument utilizes Illumina’s 2-channel sequencing by synthesis chemistry, which requires only two images per cycle, instead of the original 4-channel chemistry used by its predecessor, the HiSeq 2500. This simplified nucleotide detection reduces imaging and accelerates data processing times while preserving the same accuracy and quality found in the 4-channel chemistry.

Additional technical details on the NovaSeq instrument can be found on the Illumina website.


The Genomics Center offers all four NovaSeq flow cell options (SP, S1, S2, and the production-scale S4) as well as the XP protocol, which allows for loading of individual flow cell lanes with different library types, thereby expanding flow cell flexibility.

Novaseq flow cell comparison


The NovaSeq produces record output per flow cell combined with reduced on-instrument sequencing durations, thus dramatically improving throughput and speed over previous generations of sequencers. The immense scalability and range of applications for the NovaSeq allows for efficient sequencing of whole human, plant, and animal genomes, whole exomes, and large whole transcriptome projects at lowest per sample costs compared to other Illumina instruments.


Careful consideration of sample numbers and flow cell output is crucial for effective use of the platform. The high yields of the NovaSeq flow cells may present difficulties in efficiently filling flow cells for researchers and our intention is to introduce a lane sharing option or fractional lane purchase later this year.


Please contact Aaron Becker or Elyse Cooper at before submitting a project for the NovaSeq platform.


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Service Scale Unit Output UMN External
NovaSeq – Single-read.**
100-bp (1x100 SR) – SP flow cell. 1 1-any lane 375 M $2,002.49 $2,178.49
100-bp (1x100 SR) – S1 flow cell.2 1-any lane 750 M $3,210.82 $3,473.64
100-bp (1x100 SR) – S2 flow cell.3 1-any lane 1,800M $5,553.25 $5,982.87
NovaSeq – Paired-end.**
50-bp (2x50 PE) – SP flow cell. 1 1-any lane 375 M $2,002.49 $2,178.49
50-bp (2x50 PE) – S1 flow cell.2 1-any lane 750 M $3,210.82 $3,473.64
50-bp (2x50 PE) – S2 flow cell.3 1-any lane 1,800 M $5,553.25 $5,982.87
100-bp (2x100 PE) – SP flow cell.1 1-any lane 375 M $2,421.95 $2,669.90
100-bp (2x100 PE) – S1 flow cell.4 1-any lane 750 M $3,895.50 $4,206.79
100-bp (2x100 PE) – S2 flow cell.5 1-any lane 1,800 M $6,774.15 $7,290.98
100-bp (2x100 PE) – S4 flow cell.6 1-any lane 2,250 M $5,034.37 $5,415.02
150-bp (2x150 PE) – SP flow cell.7 1-any lane 375 M $2,622.01 $2,842.27
150-bp (2x150 PE) – S1 flow cell.8 1-any lane 750 M $4,170.85 $4,501.74
150-bp (2x150 PE) – S2 flow cell. 9 1-any lane 1,800 M $7,199.48 $7,749.69
150-bp (2x150 PE) – S4 flow cell10 1-any lane 2,250 M $5,518.03 $5,933.23
250-bp (2x250 PE) – SP flow cell.11 1-any lane 375 M $3,463.83 $3,744.05



**These runs types – 1 x100 single-read and 2 x 100 paired-end – require the purchase of the full two lanes of the flow cell. Due to the infrequent requests for these run types, there is no flow cell sharing for these runs and both lanes must be purchased.


  1. Output ≥ 375,000,000 reads x 100 bp = 37.5 Gb
  2. Output ≥ 750,000,000 reads x 100 bp = 75 Gb
  3. Output ≥ 1,800,000,000 reads x 100 bp = 180 Gb
  4. Output ≥ 750,000,000 reads x 200 bp = 150 Gb
  5. Output ≥ 1,800,000,000 reads x 200 bp = 360 Gb
  6. Output ≥ 2,250,000,000 reads x 200 bp = 450 Gb
  7. Output ≥ 375,000,000 reads x 300 bp = 112.5 Gb
  8. Output ≥ 750,000,000 reads x 300 bp = 225 Gb
  9. Output ≥ 1,800,000,000 reads x 300 bp = 540 Gb
  10. Output ≥ 2,250,000,000 reads x 300 bp = 675 Gb
  11. Output ≥ 375,000,000 reads x 500 bp = 187.5 Gb

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Data Release

There are four options for transferring data from the UMGC to clients: 1) delivery to the Minnesota Supercomputing Institute’s (MSI) high-performance file system, 2) download from a secure website, 3) download with Globus, or 4) shipment on an external hard drive. Please indicate your data delivery preference when placing an order for sequencing.

1. MSI storage

Internal clients have their data released to MSI's Shared User Resource Facility Storage (SURFS). Delivered data will be located in the "data_delivery" folder in your group's folder on MSI's primary filesystem (home/GROUP/data_delivery/umgc). MSI does not charge for SURFS storage costs, but files expire and are removed one year after they've been delivered. Files should be copied to other MSI storage locations such as Tier2, Tier3, or your group's "shared" folder before they expire. 

2. Web download

Internal clients that opt-out of MSI storage and external clients can download their data from a secure website using either a web browser or a command-line download tool, complete instructions are provided in an email from the UMGC. The client’s data is available for download for 30 days, after which the data will be removed from the data download website and the client takes responsibility for storing the data.

3. Globus

Internal and External clients can use Globus to download their data. This is the recommended method for external clients to download large datasets.

4. Hard drive

External clients may have data shipped on a hard drive purchased by the UMGC and invoiced to the client at a cost of $250 per hard drive.

Data Recovery

The UMGC archives most customer data for a year and some datasets are retained for 5 years or more. If you need a dataset re-delivered email a request to to initiate data recovery. The UMGC does not provide any guarantee that data can be successfully recovered from the archive.


How to order

Researchers can download the appropriate submission form for submitting samples or submitting client-made libraries. Once the form has been completed, please submit the submission by emailing


Illumina Sequencing Request Form (Libraries)

Illumina Sequencing Request Form (Samples)

Samples can be dropped-off at one of our laboratory locations.

1-202 Nils Hasselmo Hall (Minneapolis campus)

1-210 Cancer & Cardiovascular Research Building (Minneapolis campus)

20 Snyder Hall (St. Paul campus)

If shipping samples, the following address should be used.

Please send the tracking information to

University of Minnesota Genomics Center
1475 Gortner Ave.
28 Snyder Hall
St. Paul, MN 55108


Do you accept client-made libraries?

Yes, please consult with UMGC staff before submitting client-made libraries by emailing

We recommend that pooling be done at UMGC as PicoGreen concentrations are used for balancing libraries. However, clients may choose to pool themselves.

Client-made libraries will have the following services performed on them before proceeding with sequencing.

  1. PicoGreen (concentration of library)
  2. DNA Agilent High Sensitivity chip (size of library)
  3. KAPA QC (functionality of library)


Where should samples be shipped?

University of Minnesota Genomics Center
1475 Gortner Ave.
28 Snyder Hall
St. Paul, MN 55108