MiSeq and iSeq Sequencing


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 P2 flow cell, at 360 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.


    The UMGC offers a shared MiSeq service called Stowaway Sequencing (Stowaway-Seq). This service provides shared sequencing for researchers who need low-depth sequencing coverage. We do this by splitting a 2 x 300 bp PE flow cell into 8 “lanes” at ≤ 2M reads/lane, which users purchase on a first-come, first-served basis. Stowaway-Seq is most useful for targeted amplicon sequencing or small pilot projects to assess custom applications.

    The UMGC can barcode amplicon libraries for users (preferred). Researchers who opt to make their own custom libraries need to discuss indexing options with UMGC staff in advance of submission to avoid potential conflicts with other stowaways.

    Please see the UMGC Sequencer Home for the run schedule and our FAQs under the Guidelines tab for more details about Stowaway-Seq.  


    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 Rates

    Service Scale Unit UMN External
    MiSeq Nano - 1 M reads/lane.
    300 cycle (150 PE). 1 1-any lane $808.42  $930.40 
    500 cycle (250 PE). 2 1-any lane $898.46  $1,034.03 
    MiSeq Stowaway - 2 M reads/shared lane.
    600 cycle (300 PE). 3 1-any 1/8 lane $358.73  $412.89 
    MiSeq Micro - 4 M reads/lane.
    300 cycle (150 PE). 4 1-any lane $1,035.51  $1,191.78 
    iSeq - 4 M reads/lane.
    300 cycle (150 PE). 4 1-any lane inquire inquire
    MiSeq v2 - 8 M reads/lane.
    50 cycle (50 SR). 5 1-any lane inquire inquire
    300 cycle (150 PE). 6 1-any lane $2,022.13  $2,327.33 
    500 cycle (250 PE). 7 1-any lane $2,178.02  $2,506.75 
    MiSeq v3 - 16 M reads/lane.
    150 cycle (75 PE). 8 1-any lane $1,808.50  $2,081.43 
    600 cycle (300 PE). 9 1-any lane $2,631.98  $3,029.29 

    The Stowaway run is a shared MiSeq run designed to provide shallow (≤ 2M reads) low-cost sequencing for small-scale pilot experiments.
    In an effort to improve data quality, the output capacity for custom libraries, including amplicon libraries and low diversity applications, may generate up to 25% less data due to the addition of PhiX.

    1. Output ≥ 1 M reads x 300 bp = 0.3 Gb
    2. Output ≥ 1 M reads x 500 bp = 0.5 Gb
    3. Output ≥ 2 M reads x 600 bp = 1.2 Gb
    4. Output ≥ 4 M reads x 300 bp = 1.2 Gb
    5. Output ≥ 8 M reads x 50 bp = 0.4 Gb
    6. Output ≥ 8 M reads x 300 bp = 2.4 Gb
    7. Output ≥ 8 M reads x 500 bp = 4 Gb
    8. Output ≥ 16 M reads x 150 bp = 2.4 Gb
    9. Output ≥ 16 M reads x 300 bp = 9.6 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 next-gen@umn.edu.


    Illumina Sequencing Request Form (Libraries)

    Illumina Sequencing Request Form (Samples)

    Samples can be dropped off at one of our campus locations

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

    20 Snyder Hall (St. Paul campus)

    Samples can be shipped to the following address:

    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 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 next-gen@umn.edu to initiate data recovery. The UMGC does not provide any guarantee that data can be successfully recovered from the 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)

    Stowaway-Seq: How much space can I request?

    You may request increments of 1/8th of a MiSeq Lane to a maximum of 4 "lanes" if space allows. UMGC staff reserves the right to limit lane requests to a single "lane" per run, per user when high request volumes occur. If a large number of submissions are received, we will create multiple stowaway runs for a given submission period.

    Stowaway-Seq: What samples are acceptable?

    Libraries that have been indexed and pooled will be accepted two weeks before the Stowaway-Seq run date. We may accept samples for library creation for the stowaway service (e.g., amplicons or 16S samples), but ONLY when prior approval has been obtained, with enough time for the library creation to occur.

    Stowaway-Seq: Do you perform QC on libraries?

    Yes. We perform Kapa QC on samples to ensure a functional library.

    Stowaway-Seq: What is the deadline for a submission?

    For client-made libraries, the cut-off for submission is at least 14 days prior to the scheduled run. For amplicons and 16S samples, the cut-off for submission is at least 28 days prior to the scheduled run. Refer to Sequencer Home to see the availability of the next run.

    Stowaway-Seq: Can I request Expedited Service for a Stowaway Run?

    No. The purpose of Stowaway-Seq is not speed, but low cost. The runs are scheduled in advance and guaranteed to run on the scheduled date, in order to provide a reliable, low-cost option for all.

    Stowaway-Seq: How can I know what barcodes to use for my samples?

    Please email next-gen@umn.edu with your intended barcodes, so that they do not overlap with another researcher’s barcodes. We will check it against others currently in the run and notify you.

    Stowaway-Seq: What if I miss the deadline for submission?

    UMGC will try to accommodate your request on the next scheduled run provided there is no barcode conflict.

    Stowaway-Seq: I can't seem to get on a Stowaway-Seq run because they fill up too fast

    We have the ability to increase the frequency of Stowaway-Seq runs, and will do so if we find that demand justifies it.