Product Compatibility

Sample Information

Before preparing libraries, record information about your samples, such as sample ID and which index adapters are used for pooling. To record sample information for sequencing on the MiSeq System, use the Illumina Experiment Manager to create a sample sheet. When prompted during run setup, specify the location of the sample using the MiSeq Control Software interface

Library Preparation

Many applications are possible on the MiSeq System. For more information, see the MiSeq Applications page for a list of compatible library prep kits.

After preparing libraries according to the library prep documentation, denature and dilute libraries to a loading concentration of 6–20 pM. In practice, loading concentration can vary depending on library preparation and quantification methods.

The MiSeq 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.

MiSeq Reagents

See the MiSeq Reagent Kit support page for a complete list of MiSeq reagent kits, product compatibility, and requirements.

Analysis Options

The control software on the MiSeq System integrates with two data analysis options: MiSeq Reporter or BaseSpace.

  • MiSeq ReporterMiSeq Reporter is part of the system software suite installed on the instrument computer. As the sequencing run progresses, base call files are transferred to the output folder location. When the run is complete, the MiSeq Reporter analysis workflow specified for the run begins analysis automatically.
  • 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.

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.