MiSeq Sequencing System

Focus the power of NGS

Powerful and compact, the MiSeq System is ideal for rapid, cost-effective next-generation sequencing for virtually any lab

MiSeq Sequencing System

Speed and simplicity at your fingertips

MiSeq System is a benchtop sequencing system capable of performing a broad range of sequencing applications. Optimized sample preparation kits, push-button operation, and automated data analysis create a fast and easy end-to-end sequencing workflow for any lab.

MiSeq intuitive interface
Simple, intuitive interface

Simplicity at the touch of a button. Easy-to-follow software, onboard data analysis, and fast and easy data sharing streamlines genetic analysis on the MiSeq System.

Scientist using MiSeq system
Flexible design

With adjustable read lengths, multiple flow cell options, and choice of single or paired-end reads, the MiSeq System provides the flexibility to match data output to experimental needs.

view MiSeq runs from mobile device
Rapid turnaround time

Go from DNA to data in just over eight hours. The MiSeq System incorporates cluster generation, paired-end fluidics, sequencing by synthesis chemistry, and data analysis in a compact, all-in-one platform.

Powerful and compact sequencing system

MiSeq system specifications

System specifications

  • Output range
    540 Mb–15 Gb
  • Single reads per run
  • Max read length
    2 × 300 bp
  • Run time
    4–56 hr
  • Dimensions
    W x D x H
    68.6 cm × 56.5 cm × 52.3 cm
    (27.0 in × 22.2 in × 20.6 in)

A streamlined workflow designed for rapid turnaround time for next-generation benchtop sequencing

Manage workflow

Manage workflow seamlessly with Clarity LIMS or an existing LIMS system.

Prepare libraries

Prepare sequence-ready libraries with optimized library prep kits for targeted applications.


Generate 2 × 300 bp paired-end reads in a single run.

Analyze data

Complete analysis reports in a few hours with onboard data analysis tools.

Interpret results

Monitor and share data in real time with colleagues during a MiSeq System sequencing run.

Facilitate your research with a wide range of sequencing applications

With automated paired-end reads, an output range of up to 15 Gb per run, and optimized library prep kits, the MiSeq System can accommodate a variety of applications, including targeted gene sequencing, small genome sequencing, amplicon sequencing, 16S metagenomics analysis, and more.

MiSeq library prep

Featured applications

Compare with MiniSeq and iSeq 100 Systems


MiSeq System

MiniSeq System


iSeq 100 System

Run time 4–55 hr 4–24 hr 9.5–19 hr
Maximum output per run 15 Gb 7.5 Gb 1.2 Gb
Maximum single reads per run 25Ma 25Mb 4M
Maximum read length 2 × 300 bp 2 × 150 bp 2 × 150 bp
Data analysis offeringsc MiSeq Reporter Software, 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 MiSeq Reagent Kit v3 only.

b. For MiniSeq High Output Reagent Kit 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

Illumina DNA Prep

A fast, integrated workflow for preparing libraries for use in a wide range of sequencing applications.

MiSeq Reagent Kit v3

Optimized reagent kit that provides increased cluster density and read length, improving sequencing quality scores compared to earlier versions.

MiSeq Reagent Kits v2

Reagent kits that provide increased cluster density and read length for the MiSeq System, improving sequencing quality scores compared to v1 kits.

Speak with a specialist

Get assistance with deciding if this powerful and compact sequencing system is right for your lab. Contact us today for more information on the MiSeq System.