Product Compatibility

Requirements & Compatibility

Sample Information

Before preparing libraries for sequencing, record information about your samples, such as sample ID and which index adapters are used for pooling. Different options are available for recording information depending on how the instrument is configured. Options are BaseSpace or standalone mode.

  • BaseSpace or BaseSpace Onsite—When the system is configured for BaseSpace or BaseSpace Onsite, use the BaseSpace Prep tab. Using the BaseSpace Prep tab, you record information about the samples to be sequenced and specify sequencing run parameters. After run parameters are saved on the BaseSpace Prep tab, the run name appears on the control software interface for easy sequencing run setup.
  • Standalone mode—When the system is configured for standalone mode, use the Illumina Experiment Manager to create a sample sheet. The sample sheet is later used with third-party analysis software.

Library Preparation

Many applications are possible on the NextSeq 550 System. For more information, see the NextSeq Applications page.

After preparing libraries according to the library prep documentation, denature and dilute libraries to a loading concentration of approximately 1.8 pM. In practice, loading concentration can vary depending on library preparation and quantification methods.

The NextSeq System Denature and Dilute Libraries Guide includes a protocol for libraries that are normalized using a bead-based procedure, as well as a protocol for libraries that are normalized using standard quantification and quality control procedures. Use the appropriate protocol for the libraries you are sequencing.

NextSeq 500/550 Kits

See the NextSeq 500/550 Kit support page for a complete list of NextSeq 500/550 kits, product compatibility, and requirements.

Analysis Options

The control software on the NextSeq System integrates with BaseSpace. From the NextSeq Control Software interface, you can specify which option to use for the run.

  • BaseSpaceBaseSpace is the Illumina cloud computing environment. As the sequencing run progresses, base call files are transferred to BaseSpace. When the sequencing run is complete, log in to BaseSpace and start the BaseSpace App appropriate for the libraries that were sequenced.
  • BaseSpace OnsiteBaseSpace Onsite is a dedicated server for data analysis. As the sequencing run progresses, base call files are transferred to the BaseSpace Onsite server. When the sequencing run is complete, start the BaseSpace App appropriate for the libraries that were sequenced.
  • Standalone mode—The software generates base call files as the run progresses and writes the data to the output folder location specified for the run. No further analysis is performed.

Additional Resources

Custom Protocol Selector—Generate customized end-to-end workflow instructions based on the Illumina products you use for library prep, sequencing, and analysis.

Library Prep Kit Selector—Helps you determine the best kit for your needs based on your project type, starting material, and the method or application. Includes recommended run parameters and analysis options.

Sequencing Coverage Calculator—Helps you determine the appropriate run parameters for the desired coverage for your experiment.