NextSeq 550 Sequencing


**The NextSeq 2000 is coming to the UMGC summer 2021.**

The NextSeq 550 is a high-throughput benchtop sequencer that offers fast, one day turnaround made possible from advancements in Illumina’s 2-channel chemistry. With the ability to switch between lower and higher run configurations based on a project’s needs, the NextSeq 550 is the ideal platform for small to medium sequencing projects that range in output requirements.

This instrument expands the UMGC’s comprehensive sequencing portfolio by replacing the HiSeq 2500 rapid run as the instrument of choice for projects needing fast turnaround. Due to the growth in smaller projects that require expedited data, we purchased a second NextSeq instrument to meet demand and provide faster sequencing turnover.

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


There are two types of flow cell options (mid and high output) available with a range of outputs to accommodate a wide variety of NGS projects. Please contact us if you are interested in a read type not listed.

Next Seq table


The primary advantages of the NextSeq are sequencing speed and flexibility with run configurations. Instrument run times:

  • 12 hours for the 75-cycle mid output run
  • 30 hours for the 300-cycle high output run

In addition, users have the benefit of not needing to wait to fill a large, multi-lane flow cell before data can be generated. Whether it is mid output or high output, users purchase the full NextSeq flow cell (no lane splitting) and sequencing will begin once libraries are complete and the instrument is available. Thus, the NextSeq enables quick turnaround for many small to medium sized RNA-Seq and whole exome capture projects, as well as some whole genome applications.


Due to the 2-channel chemistry, the NextSeq does not tolerate low diversity libraries as well as other Illumina 4-channel platforms and higher spike-in concentrations of a diverse control library are required to generate high quality data. Thus, amplicon libraries with low sequence diversity should be designed with phasing bases to frame shift low diversity regions.


Please contact Aaron Becker or Elyse Cooper at for further details on the NextSeq platform.



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Service Scale Unit UMN External
NextSeq High Output Mode – Single-read.
75-bp Single-read (1x75 SR). 1 1-any lane $2,048.72 $2,404.72
150-bp Single-read (1x150 SR). 2 1-any lane $3,635.51 $4,270.83
NextSeq High Output Mode – Paired-end.
36-bp Paired-end (2x36 PE). 1 1-any lane $2,048.73 $2,404.72
75-bp Paired-end (2x75 PE). 2 1-any lane $3,635.51 $4,270.83
150-bp Paired-end (2x150 PE). 3 1-any lane $5,628.97 $6,607.67
NextSeq Mid Output Mode – Single-read.
150-bp Single-read (1x150 SR). 4 1-any lane $1,580.55 $1,855.01
NextSeq Mid Output Mode – Paired-end.
75-bp Paired-end (2x75 PE). 4 1-any lane $1,580.55 $1,855.01
150-bp Paired-end (2x150 PE). 5 1-any lane $2,351.59 $2,759.70



  1. Output ≥ 360,000,000 reads x 75 bp = 27 Gb
  2. Output ≥ 360,000,000 reads x 150 bp = 54 Gb
  3. Output ≥ 360,000,000 reads x 300 bp = 108 Gb
  4. Output ≥ 120,000,000 reads x 150 bp = 18 Gb
  5. Output ≥ 120,000,000 reads x 300 bp = 36 Gb

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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


Data Release

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

MSI storage

Internal clients and external clients that opt-in to MSI storage have their data released to the client’s MSI group directory on the MSI high-performance filesystem (/home/GROUP/data_release/umgc), from where it can be analyzed using MSI’s high-performance computers or Galaxy system. The data is stored for five years in uncompressed format with read-only permissions to avoid accidental modification, and secure off-site tape backups of the data are maintained for disaster recovery. MSI will charge the client a storage fee for this service.

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.

Hard drive

External clients may have data shipped on a hard drive purchased by the UMGC and invoiced to the client.

Data Recovery

MSI storage

MSI guarantees storage of client data for five years, after which the data can be transferred to tape for long-term storage, contact MSI ( for more information.

Web download and hard drive

Data is typically recoverable for up to 5 years. If the external researcher should ever need the FASTQ files re-posted to the data download website or shipped on a hard drive within 5 years from data release, email to initiate data recovery. The client will be charged for the cost of recovering the data from tape archive. The UMGC does not provide any guarantee that data can be successfully recovered from tape archive.


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