Local Run Manager: How do I use a custom library prep kit?

04/14/17


Local Run Manager is the onboard run planning and analysis software included on MiniSeq instruments that is used both to set up runs and perform local analysis. Note that Local Run Manager, unlike the software on the MiSeq, does not make use of sample sheets generated by Illumina Experiment Manager. Standard Illumina library prep kits are already included as built-in options in Local Run Manager. 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 software guide contains information on the required content of the custom library prep kit file, and this bulletin provides more details. To add a custom library prep kit to Local Run Manager, perform the following steps:

  1. Download the custom kit template from the Local Run Manager Downloads page.
  2. Open the template file in either Excel or a plain text editor, such as Notepad.
  3. [Kit]: This section contains the default run parameters:
    • The Name section must be unique for all kits.
    • Description: A short description of the kit. Only alphanumeric, period, dash, and space characters are allowed.
    • Available options for IndexStrategy are NoIndex, SingleOnly, DualOnly, SingleAndDual, NoAndSingle, NoAndDual, or All.
    • Available options for ReadType are Single, Paired, or All.
    • The default number of cycles for Read 1 and Read 2 are specified in DefaultReadLength1 and DefaultReadLength2, respectively.
  4. [Resources]: Custom parameters can be set here. This section is optional. For more information on available parameters, please see the “Library Prep Kits” section of the Local Run Manager software guide.
  5. [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.
    • Do not reverse complement the second index sequence. Local Run Manager will do so automatically during demultiplexing.
    • 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.
  6. Important Notes
  7. [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 software guide for a full list of available modules.
  8. Save the file, making sure to retain the format as TSV. Do not include spaces or special characters in the file name.
  9. From the Local Run Manager dashboard, click the System icon, select Library Prep Kits, and then click Add Library Prep Kit. Browse to the location of the custom kit file to add it.
  10. 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.
  11. Optional, adapter trimming: Local Run Manager will automatically perform adapter trimming for built-in Illumina kits only. To trim adapters when using a custom kit, click “+ Add custom setting” and add the Adapter option and a sequence. 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.
  12. Continue with entering the sample information and complete setting up the run.