MiSeq and iSeq Sequencing

miseq 1
photo: Courtesy of Illumina, Inc.

The Illumina MiSeq is a benchtop sequencer specialized for quick, lower-output runs on single-lane flow cells, and with the version 3 cluster chemistry, it offers Illumina’s longest read length - the 300-bp paired-end run. We commonly use the MiSeq for microbiome marker gene amplification, including 16S rRNA, fungal ITS1/ITS2, and eukaryotic 18S rRNA. This is also an optimal instrument for small genome and targeted sequencing of long amplicons.

Utilizing one-channel sequencing by synthesis technology, the Illumina iSeq gives extraordinarily fast sequencing turnaround while maintaining high data quality. It is a flexible system with a wide range of applications that is ideal for small genome sequencing, targeted and amplicon sequencing, and viral and microbial sequencing. For researchers interested in more control over their sequencing turnaround, please see our DIY iSeq service for accessing the iSeq instrument from within our lab.

See the Pricing tab for rates and outputs for the MiSeq and iSeq.


The lower throughput MiSeq and iSeq instruments are optimal for researchers needing between 1 – 16 million reads/run versus the next highest output sequencing option, the NextSeq mid output, at 120 M reads/run. And with only a single lane to scan, the MiSeq and iSeq have fast sequencing turnaround times, especially when partnered with our expedited service option.


    Cost per read is significantly higher on the MiSeq and iSeq platforms than on the NovaSeq and NextSeq instruments. In addition, amplicon sequencing, such as with 16S amplification, is commonly sequenced on the MiSeq and can be problematic due to the low diversity of the library. The UMGC mitigates this issue by increasing the amount of PhiX – a highly diverse library – into the sequencing run and lowering the cluster density, when needed. In addition, the iSeq only provides a single option of 300 cycles and 4 million reads.


    Contact Aaron Becker at next-gen@umn.edu with any questions about our low throughput sequencing options.


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    Standard Service Unit UMN External Gb M reads
    2x300 Paired-end.
    MiSeq v3 stowaway. 1/8 lane $322.14 $385.39 1.2 2
    MiSeq v3. lane $2,248.60 $2,690.07 9.6 16
    2x250 Paired-end.
    MiSeq Nano. lane $633.01 $757.62 0.5 1
    MiSeq v2. lane $1,786.25 $2,136.96 4.0 8
    2x150 Paired-end.
    MiSeq Nano. lane $560.00 $669.95 0.3 1
    MiSeq Micro. lane $748.59 $895.57 1.2 4
    iSeq. lane $895.73 $1,030.70 1.2 4
    MiSeq v2. lane $1,622.00 $1,940.44 2.4 8
    2x75 Paired-end.
    MiSeq v3. lane $1,439.50 $1,722.12 2.4 16
    1x50 Single-read.
    MiSeq v2. lane $1,304.44 $1,560.54 0.4 8

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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 next-gen@umn.edu.


    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 next-gen@umn.edu.

    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 (help@msi.umn.edu) 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 next-gen@umn.edu 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 next-gen@umn.edu.

    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