HiSeq 3000

Upgrade Resources—HiSeq 3000 to HiSeq 4000

HiSeq 4000 System Upgrade Frequently Asked Questions - Frequently asked questions about the HiSeq 4000 system upgrade.

For best results, always use compatible versions of software, reagents, and flow cell for both cluster generation on the cBot and sequencing runs on the HiSeq. For information about version compatibility, see the Version Compatibility Reference.


HiSeq 3000/4000 Cluster Kit

HiSeq 3000/4000 SBS Kit


HiSeq Control Software v3.3—The control software interface guides you through the steps to load the flow cell and reagents before beginning a sequencing run. During the run, the software provides run metrics as they are generated.

To download software for the HiSeq 3000, see HiSeq 3000 Downloads.

Real-Time Analysis 2—The HiSeq 3000 uses a new implementation of Real-Time Analysis (RTA) called RTA v2, which includes important architecture differences from RTA used on other Illumina sequencers.

For more information, see the HiSeq 3000 System Guide

Analysis Solutions

The HiSeq Control Software features an option to send run and health data to BaseSpace, the Illumina cloud computing environment. With this feature enabled, you can monitor run metrics from any location in a web browser. See the HiSeq 4000 and HiSeq 3000 Site Prep Guide for BaseSpace network considerations.

If you choose not to connect to BaseSpace, use the bcl2fastq2 conversion software to convert HiSeq 3000 output to standard FASTQ file formats for downstream analysis using third-party analysis solutions.