How to Load Barcode Indexes in Illumina® Experiment Manager

The Illumina® Experiment Manager (IEM) is an app used to create valid sample sheets for some Illumina® sequencers. Although sample sheets can be generated manually, this tool minimize the risk of errors.

By default, only Illumina® indices are preprogrammed in the software. If you are using barcodes from PerkinElmer® or other suppliers, you will need to add index information for those barcodes in IEM. The process to do this is very simple and consist of two steps

  • Load the barcode set sequences
  • Register the barcode set into the Applications folder
  1. Load the Barcode Set sequences

Go to C:\Program Files (x86)\Illumina\Illumina Experiment Manager. Within the Illumina® Experiment Manager folder you will find 4 subfolders: Applications, Genomes, Indexkits and SamplePrepKits

We will introduce in the IEM the information on the barcode inside the SamplePrepKits folder, as a text file with specific format. PerkinElmer has already generated these files for its library preparation kits. Please find the barcode/kit you are using in the table below and download the right *.txt data file indicated in the right column.

Copy the downloaded file into the SamplePrepKits folder. Now IEM can read its contents.

  1. Register the Barcode Set into the Application Folder

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

IEM stores the different applications as text files inside the Applications folder

UDI Indexes

IEM requires that the barcode sets are registered within the corresponding application file. To incorporate the NEXTFLEX® Barcode set into a specific application, open the chosen text file using a text editor such as Notepad on Windows. Open Notepad or other editors as Administrator as IEM places write protections on its files.

For example, to add the NEXTFLEX® 6nt Barcodes to Resequencing.txt

  • Right click on Notepad and select Run as Administrator, and then open the Resequencing.txt file with Notepad.
  • Find the line [Compatible Sample Prep Kits] .
  • Paste the name of the barcode set file you want to add to the list of kits appearing by default.
  • Save the file.
UDI Indexes

Now that the barcode set has been added, proceed with generating a new sample sheet for the next sequencing run as usual. When the Workflow Parameter screen appears, the NEXTFLEX® adapters will be selectable in the barcode set dropdown menu.

The following instruction guide video gives step-by-step instructions describing how to load the PerkinElmer® PG-seq™ Barcodes in Illumina® Experiment Manager.

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