Sequencing power
for every scale.
Accessible sequencing solutions for every study, every lab.

Proven sequencing technology.
Accelerate your research. Achieve your next
breakthrough.
What started as novel Illumina chemistry, sequencing by synthesis (SBS) technology,
has fueled a sequencing revolution.
Every day, researchers are using Illumina next-generation sequencing (NGS) systems to unlock
the power of the genome. Studying cancer, genetic disease, microbiology, and agriculture.
Enhancing research in emerging fields such as reproductive health and forensic science. Making
breakthrough discoveries that increase our understanding of genotypic and phenotypic variation.

A complete portfolio.
The right system for your study, your lab.

MiSeq® System
Focused power
Combining speed, high-quality data, and the longest read lengths,
the MiSeq System is ideal for sequencing targeted panels, amplicons,
and small genomes. A cost-effective alternative to capillary
electrophoresis applications, it can perform rapid sequencing and
variant detection for time-critical studies.
• Replaces capillary electrophoresis in many applications
• Offers the longest read length of any desktop system

MiSeqDx™ System
Focused Dx power
Designed specifically for clinical laboratories, the MiSeqDx System is the first
FDA-cleared in vitro diagnostic next-generation sequencing (NGS) system.
• Screening and diagnostic testing
• Data output tailored to the needs of clinical labs
• Integrated software enables sample tracking, user traceability,
and results interpretation

NextSeq® 500 System*
Flexible power
The NextSeq 500 System delivers the power of high-throughput sequencing with
the simplicity of a desktop sequencer—transforming exome, transcriptome, and
whole-genome sequencing (WGS) into everyday research tools. High-quality data
and accuracy combined with a versatile and flexible platform let you easily switch
from one application to another. Streamlined NGS workflows enable you to perform
low- and high-throughput studies to support many project sizes.
• Only desktop system capable of sequencing a human whole genome in a single run
• Configurable output and fast run time support a wide range of applications and
sample sizes
* The NextSeq 550 System has identical sequencing specifications to the NextSeq 500 System and includes array scanning
functionality for cytogenomic and karyomapping applications.

The HiSeq Series
®

HiSeq 2500 System
Production power
Offering a high-powered, cost-effective sequencing solution, the HiSeq 2500 System
enables you to quickly and economically perform large-scale high-throughput
exome, transcriptome, and WGS projects. The system can process 1 or 2 flow cells
in parallel and offers flexible run modes. These features let you adjust data output to
support your studies.
• Proven powerhouse configurable for a wide range of applications
and sample sizes
• Offers rapid and high-throughput modes for increased flexibility

HiSeq 3000 and HiSeq 4000 Systems†
Production power
Introducing a new standard in production-scale sequencing.
Building on the proven HiSeq 2500 System and now
leveraging innovative patterned flow cell technology, the
HiSeq 3000 and HiSeq 4000 Systems provide unparalleled
speed and performance. Now you can perform large-scale,
high-throughput exome, transcriptome, and WGS projects more
quickly and economically than ever before.
• Maximizes throughput
• Increases data output
• Achieves the lowest price per sample
† Available in single (HiSeq 3000 System) and dual (HiSeq 4000 System) flow cell configurations.

Find the right Illumina system for your needs. www.illumina.com/sequencer

Empowering.
Human whole-genome sequencing.
The HiSeq X™ Series. Maximum throughput.
Lowest price per genome.
HiSeq X Ten System
Population power
The HiSeq X Ten System is the first and only sequencing platform to break the $1000 barrier for a human
genome at 30x coverage. Composed of 10 or more individual instruments, the HiSeq X Ten System
is ideal for population-scale projects focused on the discovery of genotypic variation. It can rapidly
sequence tens of thousands of genomes at high coverage, delivering a comprehensive catalog of human
variation within and outside of coding regions. With its ultra-high throughput and unprecedented low price
per genome, the HiSeq X Ten System makes population-scale human whole-genome sequencing (WGS)
a reality.
• Sequences tens of thousands of human whole genomes per year
• Achieves the $1000 human genome milestone, including instrument depreciation,
sample preparation, and labor*
* Depreciation schedules and labor may differ due to differences in institutional accounting and staffing.

HiSeq X Five System
The HiSeq X Five System, a set of 5 or more individual HiSeq X Instruments, delivers fast,
affordable, production-scale human WGS. With a lower initial capital investment than
the HiSeq X Ten System, the HiSeq X Five System provides an accessible entry point to
human WGS with an upgradeable path to population-scale sequencing and the $1000
genome. Now more researchers can complete large-scale human WGS projects rapidly,
in their own labs.
• Sequences more than 9000 human whole genomes per year
• Offers an affordable price per human whole genome

Accessible sequencing solutions.
Power tailored for every researcher, application, and scale of study.

Product

Description

Key methods

MiSeq

NextSeq 500*

Focused power
Speed and simplicity for targeted and
small-genome sequencing

Flexible power
Speed and simplicity for
everyday genomics

Small genome, amplicon,
targeted gene panel sequencing

Everyday genome, exome, transcriptome
sequencing, and more

Run mode

—

Mid-output

High-output

Flow cells
processed per run

1

1

1

Output range

0.3–15 Gb

20–39 Gb

30–120 Gb

Run time

5–55 hours

15–26 hours

12–30 hours

Reads per flow cell‡

25 million§

130 million

400 million

Maximum read length

2 × 300 bp

2 × 150 bp

2 × 150 bp

* The NextSeq 550 System has identical sequencing specifications to the NextSeq 500 System and includes array scanning functionality for
cytogenomic and karyomapping applications.
† Specifications shown for an individual HiSeq X System. The HiSeq X System is available only as part of the HiSeq X Five or HiSeq X Ten System.
‡ Clusters passing filter.
§ For MiSeq Reagant Kits v3 only.

HiSeq 2500

Production power
Power and efficiency for
large-scale genomics

HiSeq 3000

HiSeq 4000

Production power
Maximum throughput
and lowest cost for
production-scale genomics

Production-scale genome, exome,
transcriptome sequencing, and more

HiSeq X Five†

HiSeq X Ten†

Population power
Maximum throughput and lowest cost
for population- and production-scale
human whole-genome sequencing

Population-scale human
whole-genome sequencing

Rapid run

High-output

—

—

—

—

1 or 2

1 or 2

1

1 or 2

1 or 2

1 or 2

10–300 Gb

50–1000 Gb

125–750 Gb

125–1500 Gb

900–1800 Gb

900–1800 Gb

7–60 hours

< 1–6 days

< 1–3.5 days

< 1–3.5 days

< 3 days

< 3 days

300 million

2 billion

2.5 billion

2.5 billion

3 billion

3 billion

2 × 250 bp

2 × 125 bp

2 × 150 bp

2 × 150 bp

2 × 150 bp

2 × 150 bp

Industry-leading data quality.
Trusted technology. Highest confidence.
Your studies deserve the best data quality. That’s what our systems are proven to deliver.
It’s no wonder more than 90% of the world’s sequencing data is generated using
sequencing by synthesis (SBS) technology from Illumina.
• Obtain the greatest accuracy with the highest percentage of sequenced bases above Q30
• Achieve the highest yield of error-free reads
• Improve efficiency with the fewest false positives, false negatives, and miscalls

The performance you need.
Every Illumina sequencing system leverages our proprietary cluster generation and SBS
chemistry, the most widely adopted sequencing technology in the world. Using a single base
extension and competitive addition of nucleotides, SBS chemistry results in highly accurate
sequencing that virtually eliminates homopolymer-related errors. You’ll get industry-leading data
quality with the highest percentage of sequenced bases above Q30, the fewest false positive
and false negative calls, and the utmost confidence in your results.
All Illumina sequencing systems perform fully automated paired-end sequencing, improving
alignment and genome assembly, and enabling accurate detection of structural variants,
gene fusions, and transcript isoforms.

> 90%
of the world’s sequencing data
is generated using
Illumina SBS technology

A wealth of library
prep solutions.
A depth of applications.
Developed to seamlessly integrate with our next-generation sequencing (NGS)
workflows, our extensive high-quality library prep solutions support the broadest
diversity of applications and sample types.

Select from a broad range of applications:*

Whole genome

Transcriptome

Exome

Amplicon

NeoPrep™ Library Prep System
Powerfully simple
Featuring the precision of digital microfluidics and unparalleled ease of use, the NeoPrep System
radically simplifies library prep. Now you can dramatically reduce hands-on time and achieve
reproducible, high-quality libraries, even with limited starting material.
• Accepts 10x lower input for some assays
• Takes just 30 minutes of hands-on time per run  
• Delivers walk-away library prep, quantification, and normalization
• Works with all Illumina sequencing systems

* Refer to www.illumina.com/neoprepsystem for a list of currently available applications.

Targeted panels

Informatics
Intuitive informatics tools
provide critical insights.
Essential data can be
transferred, stored,
analyzed, and shared
securely in BaseSpace®

Sequencing
With power for every scale,
Illumina offers a complete
portfolio of next-generation
sequencing (NGS) solutions

Library prep
In addition to manual
options, Illumina offers
the NeoPrep System for
reproducible sequencingready libraries with just
30 minutes of hands-on
time per run.

that are accessible for
every study and every lab.

Onsite or in the
BaseSpace Cloud.

Optimize with simply smart
NGS workflow solutions.
One seamless process. One complete resource.
From library prep to sequencing and informatics, Illumina offers seamless NGS workflow
solutions that optimize your process from start to finish and accelerate your progress.
As the innovators of next-generation technology, we’re here to deliver the experience
and expertise to help propel your success.

World-class solutions.
A community of support.
From sample prep, library prep, arrays, and sequencing to informatics,
Illumina next-generation solutions empower researchers and clinical researchers
across the globe to find the answers they seek.
When you join the Illumina community, you become part of a dynamic scientific
movement that includes thousands of researchers and industry thought leaders.
Throughout the year, we host user group meetings, symposia, consortia, online
forums, and other initiatives—all designed to bring the best minds together to
share ideas and advance science.
In addition to on-site training, ongoing support, and phone consults, we offer
webinars and courses at various Illumina locations. We’re here with all the
resources you need to accelerate progress.

Find the right Illumina system for your needs.
www.illumina.com/sequencer

A global genomics leader, Illumina delivers complete next-generation sequencing workflow solutions to the
basic and translational research communities. Illumina technology is responsible for generating more than
90% of the world’s sequencing data. Through collaborative innovation, Illumina is fueling groundbreaking
advancements in the fields of oncology, reproductive health, genetic disease, microbiology, agriculture,
and forensic science.
Illumina • 1.800.809.4566 toll-free (US) • +1.858.202.4566 tel • [email protected] • www.illumina.com
FOR RESEARCH USE ONLY
© 2015 Illumina, Inc. All rights reserved. Illumina, BaseSpace, HiSeq, HiSeq X, MiSeq, MiSeqDx, NeoPrep, NextSeq, and the pumpkin orange color are
trademarks of Illumina, Inc. in the US and/or other countries. All other names, logos, and other trademarks are the property of their respective owners.
Pub. No. 070-2011-003 Current as of 26 January 2015