Design sequencing experiments rapidly and efficiently with our software

Sequencing Experimental Design

Illumina offers sequencing experimental design software tools to get you started with any sequencing project. Design your experiment, set up runs, and prepare for analysis.

Our software tools help you create or import biological samples, design and pool libraries, and prepare sequencing runs directly in BaseSpace Sequence Hub. You can also create custom targeted sequencing panels for amplicon- and enrichment-based assays, and generate sample sheets. 

Design Studio

Create Targeted Sequencing Panels with DesignStudio

DesignStudio guides you through creation of Illumina targeted sequencing panels for TruSeq Custom Amplicon, Nextera Rapid Capture Custom, and Targeted RNA Expression library preparation kits. This design tool streamlines the selection of targets, submission and review of designs, and purchase of complete kits.

Learn More about DesignStudio

DesignStudio Screen Shot

Create and Manage Samples and NextSeq and MiniSeq Runs with BaseSpace Prep

Sample and run management is easy with the Prep feature for the NextSeq 500/550 and MiniSeq Sequencing Systems. This software offers an intuitive, graphical environment for one-stop library and run preparation.

Learn More about BaseSpace Prep

DesignStudio Screen Shot

Prepare MiSeq or HiSeq Runs with Illumina Experiment Manager

The Illumina Experiment Manager (IEM) software application guides you through the creation of sample sheets before a MiSeq or HiSeq sequencer run. Built-in validation checks help you minimize or eliminate any sample sheet errors.

Learn More about IEM

Additional Resources

See BaseSpace Prep in Action View Video Learn about the NextSeq 500 sequencer, and see how BaseSpace Prep helps manage sequencing runs.

DesignStudio Tutorial View Webinar Learn how to design TruSeq Custom Amplicon Panels in DesignStudio.

View Sequencing Coverage Tips

Learn how to estimate and achieve the necessary sequencing coverage for your experiment.
Learn more about: Sequencing Coverage

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Microarray Probe Design