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:
- Download the custom kit template from the Local Run Manager
- Open the template file in either Excel or a plain
text editor, such as Notepad.
[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
- 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,
[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
[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
- Do not reverse complement the second index
sequence. Local Run Manager will do so automatically during
- 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.
[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.
the file, making sure to retain the format as TSV. Do not include
spaces or special characters in the file name.
- 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
- 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
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.
- Continue with entering the
sample information and complete setting up the run.