How to add a custom library prep kit to Illumina Experiment Manager

The Illumina Experiment Manager (IEM) software is used to create and edit v1 sample sheets for Illumina systems and analysis software.

Standard Illumina library prep kits are included as built-in options in IEM. However, if not using an Illumina library prep kit, custom and third-party library prep kits can also be created, following the steps described below.

1. Navigate to the IEM folder where it is installed. The path by default is:

C:\Program Files (x86)\Illumina\Illumina Experiment Manager.

2. Add custom indexes. This step is only necessary if not using any of the Illumina indexing kits. If using an Illumina indexing kit, proceed to step 3.

a) For single index custom libraries:1. Open Indexkits folder. 2. Open any single index file; for example TruSeq DNA Single Indexes Set A.

3. Save as the file with a custom name (to avoid overwriting the original one). If unable to save due to administrator rights, save the file on the desktop and then copy it back to the Indexkits folder. 4. Open the file in a text editor, as Notepad. In the [Name] section, replace the name of the Illumina kit with the same custom kit name used to name the file. 5. Change what is needed to adjust to the desired index configuration.

• Optional: for automatic trimming, indicate the adapters sequences within the [Settings] field.

• Change the indexes names and sequences as needed.

• In the [Default Layout Single Index] field, assign the indexes according to their location on a plate making sure to assign all plate locations.

b) For dual index custom libraries:

1. Open Indexkit Folder.

2. Open any dual index file; for example TruSeq DNA CD indexes (96 indexes).

   
3. Save as the file with a custom name (to avoid overwriting the original one). If unable to save due to administrator rights, save the file in desktop and then copy it back to Indexkits folder.

4. In the [Name] section, replace the name of the Illumina kit with the same custom kit name used to name the file.

5. Change what is needed to adjust to the desired index configuration.

• Optional: for automatic trimming, indicate the adapters sequences within the [Settings] field.

• Change the indexes names and sequences as needed.

• In the [Default Layout Single Index] field, assign the indexes according to their location on a plate making sure to assign all plate locations.

  

3. Add Custom Indexes to the SamplePrepKits.

4. Open SamplePrepKits folder.

2. Open any kit file; for example TruSeq DNA Nano. 3. Save the file with a custom name (to avoid overwriting the original one). 4. In the [Name] section, replace the name of the Illumina kit with the same custom kit name used to name the file. 5. Make needed changes.

• The read length: if single read sequencing, delete the second read.

• The Compatible Index Kits section must include the name of the custom index kit created before in step 2.

4. Add Custom Kit to Applications.1. Open the Applications folder. 2. Open any Application folder file; for example Plasmids.

3. Add the SamplePrep kit name in the [Compatible Sample Prep Kits] field. 4. Save and close the file. If unable to save, save the file on the desktop with its original name, delete the original file from the IEM Application folder, and copy back the edited file.

5. Create the Sample Sheet.1. Open IEM and select create Sample Sheet. Choose the System and select Category.

2. The Custom Library and Index Kit will be displayed in the drop-down menus.

For any feedback or questions regarding this article (Illumina Knowledge Article #2346), contact Illumina Technical Support [e-mail].