Order a MiSeq System today. Speak to a representative for information on pricing, availability, and more.
Explore an ever-increasing range of sequencing applications. With flexible and simplified workflows, the MiSeq System offers a cost-effective approach for applications such as targeted resequencing, clone checking, amplicon sequencing, and RNA expression.
We are making the MiSeq Sequencing System obsolete. It will be available for order until September 30, 2025. We will continue to provide full system support through December 31, 2029. For more information, refer to PON2025-1657. The MiSeq i100 Series is the recommended alternative.
The MiSeq System requires one of the following reagent kits: MiSeq Reagent Kit v3, MiSeq Reagent Kit v2, MiSeq Reagent Micro Kit v2, or MiSeq Reagent Nano Kit v2. Each provides ready-to-use cartridge-based reagents for cluster generation and sequencing by synthesis (SBS).
Library preparation is a required sequencing step. Use our selection tool to determine the best library prep kit for your needs based on your application, method, species and more.
Identify the best approach, manage your workflow, purchase what you need, and get support.
In this video, an Illumina Field Applications Scientist discusses what to expect during the preinstallation, shipping, and delivery stages. We’ll highlight important steps in the process and introduce you to available resources.
MiSeq System
SY-410-1003
Includes one MiSeq Sequencing System with embedded touch screen monitor and on-instrument computer, dual surface imaging capability, MiSeq Software Suite, installation kits and standards, installation and training, and 12 months warranty (including parts and labor) to support automated generation of DNA clonal clusters by bridge amplification, sequencing, and primary and secondary analysis. Qualification services, instrument service plans, and reagent kits sold separately.
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MiSeq Installation and Operational Qualification
SP-103-1006
Verifies that the MiSeq System has been delivered, installed, and is operating as intended according to manufacturer specifications. Appropriate documentation is provided.
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MiSeq Performance Qualification
SP-103-1003
Verifies that the MiSeq System is performing as intended according to manufacturer specifications. Appropriate documentation is provided.
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MiSeq Operational Qualification
SP-103-1002
Verifies that the MiSeq System is operating as intended according to manufacturer specifications. Appropriate documentation is provided.
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MiSeq Disposable Wash Tubes
MS-102-9999
Includes 20 disposable wash tubes to support post-run washes that include a template line wash on the MiSeq System.
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The MiSeq System offers four different types of reagent kits (MiSeq Reagent Kit v2, MiSeq Reagent Micro Kit v2, MiSeq Reagent Nano Kit v2, and MiSeq Reagent Kit v3) to enable output levels from 850 Mb–15 Gb. This enables researchers to choose the read length and depth that best meet the needs of their applications. For more information, see the MiSeq System specification sheet.
The instrument control computer has a storage capacity of ~550 GB. To maximize storage, you can securely analyze, store, and share MiSeq data in BaseSpace Sequence Hub. BaseSpace Sequence Hub is the Illumina cloud-computing environment that eliminates the need for onsite infrastructure. Learn more about BaseSpace Sequence Hub.
The maximum output range is 13.2–15 Gb (2 × 300 bp read length) and 44–50M paired-end reads (based on cluster density) using the MiSeq Reagent Kit v3. For more information, see the MiSeq System specification sheet.
If you currently own a MiSeq System, you may be eligible for a promotion on one of the following instruments: MiSeq i100 Plus System, NextSeq 1000 System, or NextSeq 2000 System*. Experience a simpler workflow with dry instrumentation, easier run set up, expanded output, and faster secondary analysis. Complete this form to contact a sales representative and see if you are eligible.
* These promotional programs are available for a limited time. Terms and conditions apply.
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Advanced chemistry, optics, and informatics combine to deliver exceptional sequencing speed and data quality, outstanding throughput, and scalability.
Optimized reagent kit that provides increased cluster density and read length, improving sequencing quality scores compared to earlier versions.
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Reagent kits that provide increased cluster density and read length for the MiSeq System, improving sequencing quality scores compared to v1 kits.
Optimized reagent kit that provides increased cluster density and read length, improving sequencing quality scores compared to earlier versions.
An efficient, fast, and integrated library preparation workflow that yields highly accurate data for sensitive sequencing applications.
Verify instrument installation and operation, and obtain an audit-ready report from certified Illumina engineers to help meet regulatory requirements.
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