Illumina iSeq 100


Big advantages come in small packages. Measuring just one cubic foot in size, the iSeq desktop sequencer was selected as a DIY instrument due to its portability and easy-to-use system. It utilizes Illumina’s one-channel sequencing by synthesis technology to give extraordinarily fast sequencing turnaround while maintaining high data quality. Even as the smallest Illumina sequencer to date, it is still able to produce over 1.2 billion base pairs in as little as 9 hours for a 50-bp single-read run. The iSeq 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.


Low-throughput Sequencing Comparison

For researchers needing to complete small runs quickly, using the low-throughput sequencing instruments - less than 16 M reads/run - will avoid waiting for small batches of projects to pool for high-throughput sequencing on production-scale instruments. The iSeq rounds out our low-throughout sequencing options that include MiSeq stowaway runs, MiSeq nano and micro runs, and standard v2 and v3 MiSeq runs. A complete list of all low-throughput read lengths can be found here.

DIY Genomics Sequencing Comparison Options 2023

*Note: Our standard sequencing service includes data release by the Genomics Center and any trouble-shooting of runs, demultiplexing, generations of QC and FastQC files, informatics, and releasing data to MSI. These services are not available with the client-operated DIY iSeq service. Data is delivered directly to the user’s BaseSpace account.


The Genomics Center provides required training at our CCRB site under the direction of Aaron Becker – lead scientist for NGS instrumentation. Providing space is available, up to two scientists from one lab can attend the 4-hour training in CCRB at a cost of $162.58/lab. Contact to arrange for training.

Training will be a full demonstration using an actual library to give users the ability to independently sequence their own future run. Topics will cover library QC requirements through sample sheets set-up for demultiplexing, as well as run monitoring and generating FastQC reports in BaseSpace.

Reserving the iSeq

Hire iseq 100

After training, and with the guidance of the Illumina iSeq System Guide and the interface on the iSeq, clients should be able to independently use the iSeq without further support from the UMGC staff. Instrument reservations are made online and clients should select the 1-hour iSeq Instrument Loading option that will reserve the iSeq for the length of the sequencing run.

Purchasing a Cartridge

The Illumina 300-cycle iSeq reagent cartridge and flow cell are available to purchase with an EFS number at our CCRB location, or if arranged ahead of time, the frozen cartridges can be picked up at our other sites. Clients are responsible for thawing the cartridges prior to sequencing and will manage the thawing in their lab.

Library QC

There is no formal training for the QC instruments; a staff member will guide new users on the QuBit and TapeStation during their first QC sign-up session. During the iSeq training session, Aaron will go over how to use your library quantification and sizing results in the nM calculator for the final library dilution before sequencing.

QC DIY access is available in our CCRB site for both the QuBit 3.0 fluorometer for fast library quantification, as well at the Agilent TapeStation 2200 for assessing library quality. Please contact our QC team for sign-up for the DIY QC instruments and for details on QC instruments at our other sites. Alternatively, clients can submit libraries they have prepared for the Genomics Center to QC using our standard service.


Please see our DIY iSeq User Guide for further details on sequencing your own libraries. For additional questions, contact Aaron Becker @


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Required training    
Aaron Becker will guide new users through loading an actual library on the iSeq. Up to two scientists from one lab can attend the training in CCRB.1session$162.58N/A
Client operated iSeq run.    
Users independently load the iSeq at our CCRB site to fully execute their own experiment, including data upload to their BaseSpace account.12-days$207.40N/A
300-cycle cartridge.    
Cartridges are available for purchase through the Genomics Center. Users are responsible for cartridge pick up and thawing in their lab.1cartridge$621.85N/A

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Getting Started

How to sign-up

Contact Aaron Becker at to arrange for iSeq training. Once iSeq training is complete, users are able to access the instrument reservation portal to reserve the iSeq with an EFS number. Users are able to use the iSeq during CCRB lab operating hours: 9:00 AM-5:30 PM.


Sample index sheet for iSeq upload

iSeq sequencing system guide

Location for training and the iSeq

Room 1-210
Cancer and Cardiovascular Research Building
Lead: Aaron Becker
Phone: 612-624-7427
Operating Hours: 9:00 AM – 5:30 PM Monday – Friday


BaseSpace Account

Data is delivered directly to the user’s BaseSpace account. Free basic accounts include 1 TB of storage and access to a limited set of free apps for data analysis.


What consumables do I need to purchase?

The Genomics Center provides a dedicated DIY workbench in CCRB that is stocked with standard lab consumables, and we also provide a 4°C fridge with aliquoted QC supplies. Other than the iSeq cartridge, no additional sequencing reagents are needed – inside the cartridge are all the reagents needed for a sequencing run, including the denaturation reagent, primers, buffers, and cluster generation reagents. New users will need to sign-up for a free BaseSpace account for uploading their sequencing run, and also bring a flash drive for transferring their samplesheet to the iSeq. Supplies available at the workstation can be found in the DIY iSeq user guide.


Am I able to drop-off my library for the Genomics Center to sequence?

Yes! Under our standard sequencing service, clients can drop-off their library for us to sequence on the iSeq or any of our Illumina sequencing instruments. 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)

Please consult with UMGC staff before submitting client-made libraries by emailing


Is there any homework to do before the training session?

There is no formal homework for the iSeq training session, but it is recommended for clients who do not have experience preparing their own libraries to review and understand terms like indexing and pooling libraries, library sizing, library diversity, pM, and de-multiplexing. Please see the DIY iSeq user guide for a list of helpful videos on getting started with the iSeq.