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 custom sequencing and genotyping assays. This design tool streamlines the selection of targets, submission and review of designs, and purchase of complete kits.

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DesignStudio Screen Shot

Manage Samples for NextSeq and MiniSeq Runs with thePrep feature in BaseSpace Sequence Hub

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

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DesignStudio Screen Shot

Prepare NovaSeq, 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 NovaSeq, MiSeq, or HiSeq sequencer run. Built-in validation checks help you minimize sample sheet errors.

Learn More about IEM

Additional Resources

See Prep feature in BaseSpace Hub View Video Learn about the NextSeq 500 sequencer, and see how the Prep feature 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