HiSeq 4000 Compatible Products
HiSeq 4000 System
Compatible Products
Sample Information
Use Illumina Experiment Manager to record information about your samples, such as sample ID and which index adapters are used for pooling.
Cluster Generation
Cluster the flow cell on the cBot 2 System or cBot System before sequencing on the HiSeq 4000 System.
Run Components
Use the compatible version of the HiSeq Control Software (HCS) and Real-Time Analysis (RTA) software for your kits. The SBS kit pairs with either cluster kit, single read (SR) or paired-end (PE). For kit details, see HiSeq 4000 Reagent Kits.
| Cluster Kit | Software Version |
| HiSeq 3000/4000 SR Cluster Kit | HCS v3.3.52/RTA v2.7, or later |
| HiSeq 3000/4000 PE Cluster Kit | HCS v3.3.20/RTA v2.3, or later |
| HiSeq 3000/4000 SBS Kit | HCS v3.3.20/RTA v2.3, or later |
Data Analysis
Use Sequencing Analysis Viewer or BaseSpace Sequence Hub to monitor real-time quality metrics during a run.
To analyze sequencing data, choose from the following options.
- BaseSpace Sequence Hub
- bcl2fastq2 Conversion Software—Convert sequencing output for third-party analysis solutions when sequencing in Standalone mode.