All Systems

HiSeq 3000/HiSeq 4000 Systems

Choose the Right Sequencer
Choose the Right Sequencer

For tips about how to choose the best sequencer for your lab, download the Buyer's Guide to Next-Generation Sequencing Systems.

HiSeq 3000/4000: Introduction
HiSeq 3000/4000: Introduction

Overview of the HiSeq 3000/4000 workflow, patterned flow cell technology, ExAmp clustering, and best practices.
BioPharma QC
BioPharma QC

See how Merck Serono uses Illumina sequencing for biological quality control (QC) applications in biopharma production.

The Illumina Community

The Illumina Online Community

Join the Illumina Online Community. Collaborate with Illumina customers, moderators, and developers. Discuss best practices, troubleshoot, and learn about how others are using Illumina sequencers, library preparation kits, and automated data analysis to fuel their research.

Learn More

Multi-Application Sequencing

The HiSeq 3000/HiSeq 4000 Sequencing Systems build on the proven performance of the HiSeq 2500 System and leverage the patterned flow cell technology of the HiSeq X Systems to deliver high sequencing speed and performance. Offering high coverage, fast turnaround times, and the flexibility to process various sample types, the HiSeq 3000/HiSeq 4000 Systems provide a multi-application solution for production-scale genomic laboratories.

Next: Fast Sequencing for Diverse Applications

Fast Sequencing for Diverse Applications

The HiSeq 3000/HiSeq 4000 Systems deliver production-scale sequencing at a low price per sample across a range of genomic applications. The HiSeq 4000 System can sequence up to 12 genomes, 100 transcriptomes, or 96 exomes in fewer than 3.5 days. This high capacity means many samples can be sequenced simultaneously at a high depth, generating rich and meaningful data.

Explore Applications

Next: Flexible Configurations

Flexible Configurations

The dual-flow cell HiSeq 4000 System can process one or two flow cells in parallel and provides high output and daily throughput with a capacity of 1.5 Tb and 5 billion reads per run. The HiSeq 3000 System offers the same output per flow cell as the HiSeq 4000 System, but only processes one flow cell at a time, delivering 750 Gb and 2.5 billion reads per run. When throughput needs increase, the HiSeq 3000 System can be upgraded to a HiSeq 4000 System.

Next: Intuitive Bioinformatics

Intuitive Bioinformatics

Illumina offers a full range of HiSeq 3000/HiSeq 4000 software solutions to help you go from biological samples to meaningful results. BaseSpace Sequence Hub provides an integrated solution for the analysis and storage of Illumina sequencing data. With whole-genome sequencing,exome/enrichment, and RNA-Seq apps, BaseSpace Sequence Hub streamlines NGS data analysis while providing an efficient means for data storage, sharing, and transfer.

Start Over: Multi-Application Sequencing
  1.  
  2.  
  3.  
  4.  

System Specifications

105–1500 Gb
output range

2.1 million–5 billion
reads per run

2 × 150 bp
max read length

View All HiSeq 3000/HiSeq 4000 Specifications

Customer Stories

Progress in Rapid Identification of Variants Linked to Genetic Diseases
Progress in Rapid Identification of Variants Linked to Genetic Diseases

Learn how DNA sequencing is leading to progress in the rapid identification of variants that might be involved in genetic diseases. Thanks to this work, Dr. Kingsmore and his team now hold a Guinness World Records title.

View Video
GLOBAL Clinical Study Demonstrates Value of Panomics-Based Drug Discovery Approach

Integrating imaging, multiomic technologies, and big data uncovers novel diagnostic and therapeutic targets for common chronic diseases.

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
See More Customer Stories
Decade of Sequencing Graphic

One Decade of Sequencing

Explore the breakthroughs, advancements, and progress

Learn More
Interested in receiving newsletters, case studies, and information from Illumina based on your area of interest? Sign up now.

Featured Products

HiSeq 3000/4000 SBS Kit

Includes sequencing reagents specifically designed for the HiSeq 3000/HiSeq 4000 Systems. Enables production-scale sequencing for diverse applications.

View Product
HiSeq 3000/4000 PE Cluster Kit

This kit enables cluster generation for subsequent sequencing on the HiSeq 3000 and HiSeq 4000 Systems.

View Product
HiSeq 3000/4000 SR Cluster Kit

Provides reagents for Single Read (SR) cluster generation on the cBot2 System. Cluster reagents are compatible with the HiSeq 3000 and HiSeq 4000 Systems.

View Product
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.

View Product

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.

All trademarks are the property of Illumina, Inc. or their respective owners.
For specific trademark information, see www.illumina.com/company/legal.html.

© 2022 Illumina, Inc. All rights reserved.