Targeted or whole genome sequencing (WGS) approaches can be employed effectively on the Ion S5™ and Ion S5™ XL Systems for research that may help in tracing the origin of outbreaks, monitoring biologics manufacturing processes, ensuring food and beverage safety, and conducting clinical microbiology research. To get started, choose an infectious disease research application from the following table and download the appropriate user guide for the step you are interested in.

Sequencing workflow for infectious disease research


1. Select targets

2. Construct library

3. Prepare template

4. Run sequence

5. Analyze data

Targeted sequencing

Browse fixed infectious disease panels or customize your own on the Ion AmpliSeq™ Designer tool

Ion AmpliSeq™ DNA and RNA Library Preparation user guide

Ion Chef™ System:
Ion 520™ & 530™ Kit-Chef user guide

Ion 540™ Kit-Chef user guide

Ion OneTouch™ 2 System:
Ion 520 & 530 Kit-OT2 user guide

Ion 540 Kit-OT2 user guide

Ion Chef System:
Ion 520 & 530 Kit-Chef ser guide

Ion 540 Kit-Chef user guide

Ion OneTouch 2 System:
Ion 520 & 530 Kit-OT2 user guide

Ion 540 Kit-OT2 user guide

Torrent Suite™ Software v5.0 quickstart guide

Ion Reporter™ Software 5.0 help guide

Discovery and characterization


Ion Xpress™ Plus Fragment Library Kit user guide

Thermo Scientific™ MuSeek Library Preparation Kit for Ion Torrent™ user guide


Ion 16S™ Metagenomics Kit user guide

Bacterial typing research


Viral typing research

Applied Biosystems™ PathAmp™ FluA Reagents user guide

Documents and resources


User guides and FAQs


Learn more

Training, events, and webinars