# Plan a MiSeq i100 Run

Use the following instructions to plan a run for the MiSeq i100 Series systems in BaseSpace Sequence Hub.

1. Select the **Runs** tab, and then select the **New Run** drop-down.
2. Select **Run Planning**.
3. In the Run Name field, enter a unique name of your preference to identify the current run. The run name can contain a maximum of 255 alphanumeric characters, spaces, dashes, and underscores.
4. **\[Optional]** Enter a description for the run. The run description can contain a maximum of 255 characters.
5. Select your sequencing system as the instrument platform.
6. Select one of the following analysis locations.
   * **BaseSpace** — Analyze sequencing data in the cloud.
   * **Local** — Analyze sequencing data on-instrument.
7. Enter the number of cycles performed in each read:
   * **Read 1** — Enter the number of cycles for Read 1.
   * **Index 1** — Enter the number of cycles for the Index 1 (i7) primer.
   * **Index 2** — Enter the number of cycles for the Index 2 (i5) primer.
   * **Read 2** — Enter the number of cycles for Read 2.
8. Select **Next**.
9. Select your analysis application. Please note that MiSeq i100 Series only supports one analysis per planned run.
10. **\[Optional]** Enter a description for the configuration.
11. Select a library prep kit or add a new custom library prep kit as follows.
    * Select **Add Custom Library Prep Kit** under the Library Prep Kit dropdown.
    * Enter the name, read types, default read cycles, and compatible index adapter kits for your custom library prep kit.
    * Select **Create New Kit**.
12. Select an index adapter kit or add a new a custom index kits as follows. If you are using more than one library, the libraries must have the same index read lengths.
    * Select **Add Custom Index Adapter Kit** under the Index Adapter Kit dropdown.
    * Select a template type and enter the kit name, adapter sequences, index strategies, and index sequences. Make sure the second index (i5) adapter sequences are in forward orientation.
    * Select **Create New Kit**.
13. If applicable to your application, select a reference genome.
14. Select **Next** to configure secondary analysis settings.