Local Run Manager v1.3 for MiniSeq How to use a custom library prep kit

Important note: Version 2 of Local Run Manager is available on-instrument for MiniSeq sequencers that have been updated to MiniSeq Control Software 2 and Windows 10. This bulletin applies only to MiniSeqs running version 1 of the control software on Windows 7, which comes pre-installed with Local Run Manager version 1. Local Run Manager version 2 is also available for installation off-instrument and use with MiniSeq data from either version of control software.MiniSeq instruments with version 1.3 of Local Run Manager as the integrated onboard software for run planning and analysis come with some Illumina library prep kits as built-in options. Version 1.3 of Local Run Manager for MiniSeq does not make use of sample sheets generated by Illumina Experiment Manager, but can import custom kit definitions. Before custom and third-party library prep kits can be used, they must be uploaded to Local Run Manager via a custom library prep kit file prior to setting up a run. The Local Run Manager version 1.3 for MiniSeq software guide contains information on the necessary content of a custom library prep kit file and this bulletin provides more details.

To add a custom library prep kit to Local Run Manager version 1.3 for MiniSeq, perform the following steps:

1. Download the Local Run Manager Custom Library Prep Kit Template and open the file in either Excel or a plain text editor, such as Notepad.

2. Edit the fields as follows:

   1. [Kit]: This section contains the default run parameters:

      1. The Name section must be unique for all kits.

      2. Description: A short description of the kit. Only alphanumeric, period, dash, and space characters are allowed.

      3. Available options for IndexStrategy are NoIndex, SingleOnly, DualOnly, SingleAndDual, NoAndSingle, NoAndDual, or All.

      4. Available options for ReadType are Single, Paired, or All.

      5. The default number of cycles for Read 1 and Read 2 are specified in DefaultReadLength1 and DefaultReadLength2, respectively.

   2. [Resources]: Set custom parameters here. This section is optional. For more information on available parameters, see the “Library Prep Kits” section of the Local Run Manager version 1.3 for MiniSeq software guide.

   3. [Indices]: Specify which index sequences will be used with this kit. Include the Name along with the Sequence and IndexReadNumber (1 or 2). After loading the custom kit into Local Run Manager, sequences are selected using the Name value.Important Notes:

      1. Do not reverse complement the second index sequence. Local Run Manager will do this automatically during demultiplexing.

      2. Mixing indexing lengths and types (dual and single) within a kit and run is not supported. Index lengths must be consistent and only A, G, C, and T bases are valid. N cannot be entered and used as a wildcard.

      3. Index names are limited to six characters. Index names longer than six characters will prevent the run from being saved.

   4. [SupportedModules]: Include the name of the analysis module or modules which can make use of this kit when creating a run. Multiple modules should be included on separate lines. The full module name must be used, with no spaces, such as GenerateFastQWorkflow. Please refer to the Local Run Manager version 1.3 for MiniSeq software guide for a full list of available modules.

3. Save the file, making sure to retain the format as TSV. Do not include spaces or special characters in the file name.

4. From the Local Run Manager dashboard, select the System icon, select Library Prep Kits, and then select Add Library Prep Kit. Browse to the location of the custom kit file to add it.

5. From the dashboard, create a new run. In the Run Settings section select your custom kit from the Library Prep Kit dropdown menu then enter the read length information.

6. Adapter trimming (optional): Local Run Manager for MiniSeq will automatically perform adapter trimming for built-in Illumina kits only. To trim adapters when using a custom kit, select “+ Add custom setting” and add the Adapter option and a sequence.

• Important Note: Because adapter trimming is not specified in the kit file, this setting must be included for each new run. For paired-end reads with a different Read 2 adapter, add another line with AdapterRead2 and a sequence. The example below shows the TruSeq™ adapter sequences.

1. Continue with entering the sample information and complete setting up the run.

Note: Kit definitions released for version 2 of Local Run Manager can still be imported and used with version 1.3 of Local Run Manager for MiniSeq, but for unique dual (UD) index kits the by-well selections cannot be used with version 1.3. UD index combinations can still be selected per index.

For any feedback or questions regarding this article (Illumina Knowledge Article #1320), contact Illumina Technical Support [e-mail].