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MiSeq System

Methods Guide
Methods Guide

All the information you need, from BeadChips to library preparation to sequencer selection and analysis. Select the best tools for your lab.
AmpliSeq for Illumina Sequencing Solution
AmpliSeq for Illumina Sequencing Solution

Delivers a range of ready-to-use and custom panels for simple, flexible targeted resequencing that provides high-quality data you can trust.
Enabling Human Microbiome Studies
Enabling Human Microbiome Studies

See how 16S rRNA sequencing on the MiSeq System enables studies like The American Gut Project.

Broad Applications Base

The MiSeq System facilitates your research with a wide range of sequencing applications. It is capable of automated paired-end reads and up to 15 Gb per run, delivering over 600 bases of sequence data per read. The library prep kits that it uses are optimized for a variety of applications, including targeted gene, small genome, and amplicon sequencing, 16S metagenomics, and more.

Explore Applications

Next: Integrated, Optimized Library Prep

Integrated, Optimized Library Prep

Library prep kits prepare input RNA or DNA for a diverse range of applications such as whole-genome and targeted region resequencing, transcriptome analysis, and expression profiling. Each library prep method is optimized to fit each unique application, and most are available in a variety of throughput and multiplexing configurations.

Next: Simple NGS Workflow

Simple NGS Workflow

The MiSeq System can go from DNA to data in just over 8 hours. A compact, all-in-one platform incorporates cluster generation, paired-end fluidics, sequencing by synthesis chemistry, and data analysis. An intuitive touch screen and plug-and-play reagents with RFID tracking add convenience. The MiSeq System eliminates the need for auxiliary hardware and computing resources, saving valuable lab bench space. Seamless data upload to BaseSpace Sequence Hub enables analysis, collaboration, and security.

Next: User-Friendly, Intuitive Software

User-Friendly, Intuitive Software

System software guides you through sample sheet creation and setup prior to a run, then walks you through flow cell and reagent loading steps. Control software overviews quality statistics you can monitor as the run progresses. Once primary analysis completes, reporting software launches and automatically analyzes the data quality and coverage information of each sample.

Start Over: Broad Applications Base
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Workflow

 
Prep

Library prep kits are optimized for targeted applications.

 
Sequence

MiSeq System can generate 2 × 300 bp paired-end reads in a single run.

 

 
Analyze

Selected analysis initiates automatically, completes in a few hours, then generates a report.

 
Share

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

See MiSeq Application-Specific Workflows

System Specifications

540 Mb–15 Gb
output range

1-25 million
reads per run

2 × 300 bp
max read length

View All MiSeq Specifications

Customer Stories

Of Humans and Microbes: a Long Lasting Relationship
Of Humans and Microbes: a Long Lasting Relationship

Researchers analyzed fecal samples from humans, chimpanzees, bonobos, and gorillas to demonstrate that hominids and certain gut colonizing bacteria co-evolved.

View Video
Seeking the Source of Bacterial Drug Resistance

A targeted deep sequencing assay identifies multidrug-resistant tuberculosis strains responsible for silent outbreaks.

Read Article
Agriculture Throughout the World is Benefiting from the Latest NGS Technologies

Texas A&M AgriLife uses the NovaSeq 6000 and iSeq 100 Systems to provide high-quality plant, animal and insect genome data to its partners worldwide.

Read Article
Read More Stories

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Featured Products

MiSeq Reagent Kit v3
MiSeq Reagent Kit v3

Optimized chemistry to increase cluster density and read length, and improve sequencing quality scores, compared to earlier MiSeq reagent kit versions.

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MiSeq Reagent Kits v2
MiSeq Reagent Kits v2

MiSeq sequencing reagents in pre-filled, ready-to-use cartridges. Micro and nano formats are available for low output applications.

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Nextera XT DNA Library Preparation Kit
Nextera XT DNA Library Preparation Kit

Prepare sequencing libraries for small genomes, PCR amplicons, plasmids, or cDNA in as little as 90 minutes, with a low DNA input requirement.

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Related Solutions

For Research Use Only

Not for use in diagnostic procedures (except as specifically noted).

Innovative technologies

At Illumina, our goal is to apply innovative technologies to the analysis of genetic variation and function, making studies possible that were not even imaginable just a few years ago. It is mission critical for us to deliver innovative, flexible, and scalable solutions to meet the needs of our customers. As a global company that places high value on collaborative interactions, rapid delivery of solutions, and providing the highest level of quality, we strive to meet this challenge. Illumina innovative sequencing and array technologies are fueling groundbreaking advancements in life science research, translational and consumer genomics, and molecular diagnostics.

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