The HiSeq 3000/HiSeq 4000 Systems have been discontinued. We will continue to provide full support of the instruments and supply the reagents through February 28th, 2023 (for the HiSeq 3000 System) or March 31, 2024 (for the HiSeq 4000 System). To find an alternative instrument, we recommend using the Sequencing Platform Comparison Tool.
HiSeq 3000/HiSeq 4000 Resources
System Literature
Product Selection and Experiment Planning Tools
Find tools to help you choose the right products for your needs and plan your experiments. Identify the right library prep kit or microarray, calculate sequencing coverage, explore methods compiled from publications, design custom assays, and more.
Explore Tools
Education and Support Resources
HiSeq 3000 User Guide
Describes instrument components, on-instrument software, the sequencing workflow, and maintenance procedures for the HiSeq 4000.
Sequencing Online Training
Online Illumina sequencing courses are free, interactive, and available any time.
Personalized Training Workflow Selection Tool
This tool will help you determine the best hands-on sequencing training for your needs based on your area of interest, application, library preparation kit, and platform.
HiSeq 4000 User Guide
Describes instrument components, on-instrument software, the sequencing workflow, and maintenance procedures for the HiSeq 4000.
Sequencing Coverage
Sequencing coverage describes the average number of NGS reads that align to known reference bases. Coverage requirements vary by application.
Quality Scores
Additional information about sequencing quality scores, how they are calculated, and the relationship between quality score and base call accuracy.
HiSeq 3000/HiSeq 4000 Site Prep Guide
The site prep guide contains lab specifications and requirements for preparing the lab for sequencing on the HiSeq 3000 or HiSeq 4000 System.
Sequencing Troubleshooting Tips
These short videos provide expert tips for common sequencing issues such as overclustering and inconsistent quantitation.
Custom Protocol Selector
The Custom Protocol Selector enables you to generate your own customized documentation, specifically tailored to your experiment.
HiSeq 3000 Support Documentation
Access guides, literature, and technical notes for the HiSeq 3000 System.
HiSeq 4000 Support Documentation
Access guides, literature, and technical notes for the HiSeq 4000 System.
Customer Stories
Progress in Rapid Identification of Variants Linked to Genetic Disease
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.
Watch VideoExploring the Genetic Basis of Oral Cancer
Researchers in India study a deadly oral cancer that is strongly associated with chewing tobacco together with slaked lime.
Read articleGLOBAL 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 articleVideos and Webinars
Illumina High Throughput Sequencing Portfolio Video
Increase your throughput and coverage depth with the increased capacity of the HiSeq 3000 and HiSeq 4000 Systems.
Leveraging Patterned Flow Cell Technology
Learn how to harness the power of the HiSeq 3000 and HiSeq 4000 Systems for your diverse high-throughput sequencing applications.
Human Genetics and Cancer Genomics
Discover how linked-reads and phased genome analysis provide insights in human genetics and oncology.
Exome Sequencing on the HiSeq 4000 System
Demonstration of high-throughput NGS methods on the HiSeq 4000 instrument, focusing on the exome sequencing workflow.
Core Facility Case Study
Learn how the UCSF Center for Advanced Technology transitioned from the HiSeq 2500 System to the HiSeq 4000 System.