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