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Ion Torrent Next-Generation Sequencing Data Analysis Workflow

Ion Torrent NGS software overview

Ion Torrent sequencing is enabled by a suite of software tools every step of the way. See below for various stages of an NGS workflow and the Ion Torrent Software that is utilized.

Workflow step NGS system:
Ion GeneStudio S5		 NGS system:
Ion Torrent Genexus Integrated Sequencer		 What it does
Panel design Ion AmpliSeq Designer Ion AmpliSeq Designer Design custom targeted sequencing panels
Run planning & sequencing Torrent Suite Software Genexus Software Plan, monitor, and manage sequencing runs
Primary analysis Torrent Suite Software Genexus Software Process raw sequencing data, review run metrics, align reads, and generate analysis outputs
Variant analysis Ion Reporter Genexus Software Call, annotate, filter, and prioritize variants
Interpretation & reporting Ion Reporter Genexus Software Investigate oncology research biomarkers and create customizable reports

Why use an integrated informatics workflow?

An integrated workflow can help research teams connect sequencing data analysis steps more clearly, from panel design through downstream review.

  • Clearer handoff between workflow stages
  • More structured review of run quality and variants
  • Better organization of research outputs
  • Improved navigation across related resources

Ion Torrent Informatics and Sequencing Software

Each software option supports a specific part of the research workflow. Use the cards below to identify which tool fits your current analysis need.

Ion AmpliSeq Designer

Panel design

Supports research panel design with ready-to-use, on-demand, or made-to-order panel options.

  • Select targets
  • Customize panel content
  • Prepare for downstream sequencing

Torrent Suite Software

Primary analysis

Supports automated primary data analysis for Ion Torrent sequencing runs and run-level quality review.

  • Process sequencing run data
  • Review quality information
  • Prepare for variant analysis

Ion Reporter Software

Variant review

Helps researchers annotate, filter, and prioritize variants of interest for research review.

  • Annotate variants
  • Apply filters
  • Organize research results

Ion Torrent Plug-ins

Plug-ins

Expand software functionality with integrated or open-source capabilities.

  • Add specialized functionality
  • Extend analysis workflows
  • Review compatibility

Genexus Software

Integrated analysis

An integrated software for NGS run planning, analysis and reporting with

  • Genexus Integrated Sequencer
  • Sample to report integration  
  • Automatic back-up and encryption
  • Customizable reports

NGS software support

Guides and troubleshooting

Find help for Ion Torrent NGS workflows, software, and data analysis.

  • Getting started with the informatics workflow
  • Troubleshooting common sequencing and analysis questions
  • User guides and release notes
  • Resources for analyzing and archiving data

Ion Torrent NGS data analysis frequently asked questions

Torrent Suite software supports primary data analysis for Ion GeneStudio S5 Systems. Genexus software support primary analysis for Genexus System

Ion Reporter Software provides bioinformatics tools for analyzing, annotating, filtering, and reviewing Ion Torrent sequencing data. Preconfigured and customizable analysis workflows help researchers identify and prioritize variants of interest and generate downstream analysis results and reports

Ion AmpliSeq Designer is a web-based tool for designing custom targeted sequencing panels. Researchers can specify genes or genomic regions of interest and use the tool to create Ion AmpliSeq panel designs for compatible targeted sequencing workflows.

Yes. Plug-ins can extend Torrent Suite and selected Ion Torrent analysis workflows with additional analysis and data-processing capabilities. Available plug-ins and compatibility depend on the software version and application

For Research Use Only. Not for use in diagnostic procedures.

PMR-010277