Product Compatibility

Sample Information

Use the Illumina Experiment Manager to record information about your samples, such as sample ID and which index adapters are used for pooling. 

Library Preparation

See MiSeq Applications for possible applications

After preparing libraries, denature and dilute libraries to a loading concentration of 6–20 pM. See the MiSeq System Denature and Dilute Libraries Guide for instructions.

Flow Cell and Software Requirements

Flow Cell

Cap Color

Required MCS Version

Standard Flow Cell in MiSeq Reagent Kit v3 (19 tiles)

Clear cap

MCS v2.3, or later

PGS Flow Cell in MiSeq Reagent Kit v3 (19 tiles)

Clear cap

MCS v2.4, or later

Standard Flow Cell in MiSeq Reagent Kit v2 (14 tiles)

Clear cap

MCS v2.0, or later

Micro Flow Cell in MiSeq Reagent Micro Kit v2 (4 tiles)

Green cap

MCS v2.1, or later

Nano Flow Cell in MiSeq Reagent Nano Kit v2 (2 tiles)

Yellow cap

MCS v2.0, or later

Analysis Options

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.