The Illumina HiSeq® 4000 Sequencing System is a high-throughput next-generation sequencing (NGS) platform designed for large-scale genomic analysis, population studies, and high-volume sequencing workflows. Despite its age, the HiSeq 4000 remains actively used in research environments due to its robust hardware, proven sequencing performance, and the availability of open-source tools that enable continued operation and workflow control.

In addition to Illumina’s well-established sequencing-by-synthesis (SBS) chemistry and patterned flow cell technology, the HiSeq 4000 benefits from an open-source software toolkit published in Scientific Reports (Nature Research). This peer-reviewed toolkit enables laboratories to continue operating the HiSeq 4000 outside of legacy vendor software constraints, extending the usable life of the system for research, method development, and cost-sensitive sequencing projects.

This open-source approach allows technically capable labs and genomics cores to:

• Maintain operational control of the instrument

• Support customized workflows and automation

• Continue high-throughput sequencing without reliance on deprecated software ecosystems

The HiSeq 4000 is optimized for whole-genome sequencing, whole-exome sequencing, RNA-Seq, ChIP-Seq, metagenomics, and large cohort studies, delivering reliable data quality and consistent throughput across long production runs.

Common Applications

• Whole-genome sequencing (WGS)

• Whole-exome sequencing (WES)

• RNA sequencing (RNA-Seq)

• ChIP-Seq and epigenetics research

• Metagenomics and microbiome analysis

• Large-scale population and cohort genomics

• Translational and academic research

Key Features & Highlights

• High-throughput NGS sequencing system

• Patterned flow cell technology for increased data density

• Illumina sequencing-by-synthesis (SBS) chemistry

• Proven, durable hardware platform with extensive global install base

• Open-source toolkit available (peer-reviewed, Nature Scientific Reports)

• Enables continued use for research-focused laboratories

• Ideal for genomics cores, biotech R&D, and method development

Open-Source Software Support (Important)

A peer-reviewed open-source toolkit has been published in Scientific Reports (Nature) specifically enabling continued operation and workflow control of the Illumina HiSeq 4000. This makes the system particularly attractive for labs with in-house bioinformatics or engineering expertise seeking long-term value from high-throughput sequencing hardware.

(Reference available upon request; publication provided by buyer.)

Included / Not Included

• Illumina HiSeq 4000 Sequencing System (configuration as shown)

• Flow cells, reagents, consumables not included unless explicitly stated

• Computing infrastructure, servers, and data analysis pipelines not included

• Software availability depends on buyer implementation (open-source supported)

Warranty, Service & Support

This HiSeq 4000 is offered with a 30-day warranty for added buyer confidence. We also provide service contracts, preventative maintenance options, and flexible payment plans to support academic institutions, genomics cores, and commercial research labs.

Condition & Notes

Unit is offered as preowned genomic sequencing equipment unless otherwise specified. Buyers are encouraged to review photos and contact mLab Supply to confirm configuration, facility requirements, electrical needs, and service options prior to purchase.