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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.

The MiSeq Online Community

Join other MiSeq owners in the MiSeq Online Community. Collaborate with Illumina moderators and MiSeq owners. Discuss best practices, troubleshoot, and learn about how others are using MiSeq preparation kits, push-button sequencing, and automated data analysis to fuel their research.
Join Now

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
Large-Scale Bull Genome Sequencing Enables Rapid Livestock Improvement

WGS data from the 1000 Bull Genomes Project is aiding discoveries of positive and negative traits, benefiting herds globally.

Read Article
eDNA Sequencing Offers a Powerful Lens to View Changes in Biodiversity

NGS and eDNA metabarcoding enable researchers to monitor a variety of ecosystems accurately.

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.

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.

AmpliSeq for Illumina Focus Panel
AmpliSeq for Illumina Focus Panel

Targeted DNA and RNA research panel investigating 52 genes with known relevance to solid tumors.

View All MiSeq Products

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