Transitioning from Ion Torrent Next-Generation Sequencing Systems to Illumina Sequencing Platforms

Step-by-step, workflow transition guidance from Illumina Support experts tailored to users new to Illumina systems.


Transitioning to a new NGS workflow requires careful planning. And importantly, the path to implementation will vary by user depending on the current solution being used and the particular set of needs that must be addressed. For this reason, a customized support resource providing the right information at each step can be helpful in ensuring an efficient, rapid, and smooth experience.

Towards that end, this webpage supports the transition from Ion Torrent Next-Generation Sequencing Systems to Illumina Sequencing Platforms. For each step of this process you will find key questions and answers that outlines and addresses top considerations and concerns based on input from Illumina Support and fellow users.

Transition Process



Initial Considerations
  • Common questions
  • Guidance on planning a transition
Workflow Considerations
  • What is the same and what is different?
  • Is new equipment needed?
Panel Design and Ordering
  • How to design a custom panel for use on Illumina systems
  • What AmpliSeq for Illumina Panels are available?
Implementation Best Practices for Library Preparation, Sequencing, and Analysis
  • Key considerations
  • Differences to expect

Additional Support Resources

Visit the AmpliSeq for Illumina panel support pages on the Illumina website for documentation, software downloads, training resources, and information about compatible Illumina products.

Concierge support is available to current and new-to-Illumina customers. Reach out to your local Illumina field representative (ie TAM, Sales Specialist, Library Prep Specialist, FAS, etc.) to engage with Concierge.

From advanced content design to data analysis, custom bioinformatics and training, design support by Illumina Concierge can help improve coverage and enable add-on or nonhuman species designs. Researchers can also assess the AmpliSeq for Illumina targeted resequencing solution with their own samples on an Illumina sequencing system before investing. Custom Bioinformatics can assist with custom app and pipeline design. Trained and certified scientists offer library preparation training at customer sites.