IEM Configuration

This repository contains configuration files for the Illumina® Experiment Manager (IEM) for third-party indices. Adding these files to your IEM configuration will allow you to create SampleSheets using IEM for third-party library kits.

The configuration files were created for use with IEM 1.19.1 following the instructions in the IEM Software Guide from January 2021.

The files are provided as a courtesy to users of the varvis® software. They are free to use for anybody else. Feedback or feature requests are always welcome.

Disclaimer

The configuration files are provided "as is" and the authors make no representations or warranties of any kind concerning suitability, correctness or functionality. These files are not part of the medical device varvis®.

Links to other websites are provided as a convenience and do not indicate any endorsement or business relationship.

Download

Please download the latest version from releases. ZIP archives containing all configuration files are provided there.

Installation

IEM is typically installed into a directory such as this:

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

The IEM program directory contains four directories:

Applications
Genomes
IndexKits
SamplePrepKits

Copy the files from the directories in this repository into the respective directory of IEM on your computer. Then, restart IEM.

Note that you will probably need administrator rights on your computer in order to modify files in the program directory.

Available index adapters

Name	Manufacturer	Length/ nt	SamplePrepKit	IndexKits
IDX96	Nimagen	10	Nimagen UDI	Nimagen IDX96-U01 Nimagen IDX96-U02v2 Nimagen IDX96-U03 Nimagen IDX96-U05 Nimagen IDX96-U06
IDX96	Nimagen	8*	Nimagen UDI	Nimagen IDX96-U01-8nt Nimagen IDX96-U02v2-8nt Nimagen IDX96-U03-8nt Nimagen IDX96-U05-8nt Nimagen IDX96-U06-8nt
IDX96	Nimagen	8*	Nimagen UDI	Nimagen IDX96-U01-RC-8nt Nimagen IDX96-U02v2-RC-8nt Nimagen IDX96-U03-RC-8nt Nimagen IDX96-U05-RC-8nt Nimagen IDX96-U06-RC-8nt
16-UDI	Twist Bioscience	10	Twist Enrichment UDI	Twist 16 UDI
96-UDI	Twist Bioscience	10	Twist Enrichment UDI	Twist 384 UDI Twist 96 UDI Plate A Twist 96 UDI Plate B Twist 96 UDI Plate C Twist 96 UDI Plate D
IDT 8nt	IDT	8	IDT UDI 8nt UMI	IDT UDI 8nt UMI Set A IDT UDI 8nt UMI Set B IDT UDI 8nt UMI Set C IDT UDI 8nt UMI Set D IDT UDI 8nt UMI 384 Indices

*Some Nimagen amplicon designs require to use at least 151 cycles for Read 1 and Read 2. This is not compatible with 10nt indices on most devices. Nimagen states, however, that their 10nt index plates can be used as 8nt indices. For convenience, we created configurations with 8nt from those index plates. Please note that you must select different configurations depending on your device, for example:

• Nimagen IDX96-U01-8nt for the Forward Strand Workflow implemented in MiSeq and NovaSeq (v1.0 reagents),
• Nimagen IDX96-U01-RC-8nt for the Reverse Complement Workflow implemented in NextSeq and NovaSeq (v1.5 reagents).

See also the Indexed Sequencing Overview Guide Document #15057455 (v08 Nov 2020).

Illumina® is a registered trademark of Illumina, Inc. All other trademarks are property of their respective owners.