iSeq 100 Sequencing System

Expand your research

Harness the power of Illumina next-generation sequencing (NGS) technology in an easy-to-use, inexpensive ecosystem right in your lab

iSeq 100 sequencing system

Meet your new lab partner

Get a behind-the-scenes look at the most affordable, compact benchtop sequencing system in the Illumina portfolio and see how easy it is to harness the power of NGS in your lab.

sequencing on iSeq 100 sequencing system
Harness the power of NGS

Leveraging the speed and affordability of complementary metal-oxide-semiconductor (CMOS) technology and the accuracy of sequencing by synthesis (SBS) chemistry, the iSeq 100 System enables virtually any lab to acquire powerful NGS technology.

iSeq 100 reagent
Deeper insights with NGS

By providing both higher data resolution and deeper coverage compared to qPCR and Sanger sequencing, the iSeq 100 System allows greater statistical confidence for calling variants or low-frequency alleles with faster time to results and fewer hands-on steps.1,2

iSeq 100 sequencing run
Enhance efficiency and autonomy

Compared to larger sequencing systems or outsourcing, the iSeq 100 System provides faster and cost-effective small-scale runs, independence from outsourcing, and control of the sequencing process from beginning to end.

iSeq loading reagents
Flexibility at your fingertips

With a maximum output of 1.2 Gb for longest supported read length, the iSeq 100 System offers rapid, multiplexed sequencing for a range of DNA and RNA sequencing applications, including small-genome sequencing, targeted gene sequencing, and gene expression profiling.

Implementing Illumina NGS is a lot easier than you think

Viromics laboratory lead scientist Dr. John-Sebastian Eden from the Westmead Institute for Medical Research has brought his sequencing projects in-house. Learn why and how he decided on the iSeq 100 System.


Simply powerful

iSeq 100 instrument specifications 

System specifications

  • Max output
    1.2 Gb
  • Single reads per run
  • Max read length
    2 × 150 bp
  • Run time
    9.5–19 hr

A comprehensive, streamlined workflow

A comprehensive, streamlined workflow that makes the iSeq 100 System ideal for any lab seeking to perform rapid and cost-effective genetic analysis.

Manage workflow

Manage your workflow seamlessly with Clarity LIMS software or your existing LIMS system.

Prepare libraries

Prepare libraries for a range of applications with high-performance library preparation kits.


Generate sequences with ready-to-use reagents featuring proven Illumina sequencing by synthesis chemistry in as little as 9.5 hr.

Analyze data

Monitor and analyze sequencing runs using the on-instrument software, Local Run Manager, and touch-screen interface.

Interpret results

Interpret and share results using apps located on BaseSpace Sequence Hub.

Designed with versatility in mind

With a maximum output range of up to 1.2 Gb per run, optimized library prep kits, and high resolution and analytical sensitivity, the iSeq 100 System is a versatile option for a range of applications, including small-genome sequencing, 16S metagenomics studies, gene editing validation, and more.

iSeq 100 ready to start sequencing run

Featured applications

Using the iSeq 100 System for quality control

Charlie Johnson, the director of genomics and bioinformatics at Texas A&M AgriLife, discusses how his lab pairs the iSeq 100 Sequencing System with the NovaSeq 6000 Sequencing System for quality control and why the iSeq 100 System has become critical to their workflow.

Compare with other benchtop sequencing systems


iSeq 100 System

MiniSeq System


MiSeq System

Run time 9–19 hr 4–24 hr 5–55 hr
Maximum output per run 1.2 Gb 7.5 Gb 15 Gb
Maximum single reads per run 4M 25Ma 25Mb
Maximum read length 2 × 150 bp 2 × 150 bp 2 × 300 bp
Data analysis offeringsc BaseSpace Sequence Hub, Illumina Connected Analytics, on-premises DRAGEN server BaseSpace Sequence Hub, Illumina Connected Analytics, on-premises DRAGEN server BaseSpace Sequence Hub, Illumina Connected Analytics, on-premises DRAGEN server

a. For MiniSeq High Output Reagent Kit only.

b. For MiSeq Reagent Kit v3 only.

c. A dedicated DRAGEN server is paired with an Illumina sequencing system and can be used to plan secondary analysis as part of a sequencing run using the Illumina Run Manager. An on-premises DRAGEN server does not communicate directly with the sequencing system but can ingest and process data from any Illumina sequencing system via a command-line.

Popular products

iSeq 100 Reagents

Reagents for the iSeq 100 System feature a ready-to-use cartridge with one-channel SBS chemistry and CMOS technology for simple, low-cost sequencing.

PhiX Control v3

PhiX Control v3 is a ready-to-use control library for Illumina sequencing runs.

New to next-generation sequencing?

Learn about next-generation sequencing

Find educational and support resources to help you learn about next-generation sequencing (NGS) and select the right products for starting your sequencing project.

Get started with the iSeq 100 System

Learn how to get started with the iSeq 100 System using step-by-step guides and training videos. See how easy it can be to bring NGS to your lab.

Software for the iSeq 100 System

We have taken most of the manual work out of the NGS data analysis process. Local Run Manager software is installed on every iSeq 100 System and automatically performs on-instrument data analysis. The software has a user-friendly touch-screen interface for starting a sequencing run, monitoring run status, viewing results, and analyzing data.

Installation and support

The iSeq 100 System is easy to install on your own. A variety of support resources are available to help you get started. Illumina scientists and engineers are at hand to provide support and training, either online or in person, to help bring laboratory personnel quickly up to speed. For long-term maintenance, the system is covered by a one-year warranty that includes a replacement instrument or field service engineer support (depending on region) to minimize downtime.


  1. Precone V, Del Monaco V, Esposito MV, et al. Cracking the code of human diseases using next-generation sequencing: Applications, challenges, and perspectives. BioMed Res Int. 2015;2015:161648. Published 2015 Nov 19. doi:10.1155/2015/161648 
  2. Shokralla S, Porter TM, Gibson JF, et al. Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform. Sci Rep. 2015;5:9687. Published 2015 Apr 17. doi:10.1038/srep09687

Ready to expand your research?

Get assistance with deciding if your lab can benefit from this small and powerful benchtop sequencing system. Contact us today for more information on the iSeq 100 System.