Ion Torrent secondary analysis

Ion Torrent data handling and analysis

Depending on the sequencing application, Ion Torrent data is/can be analysed using either Torrent Suite Software analysis modules or cloud based Ion Reporter Software.

Torrent Suite Software

Ion S5 XL instrument is handled via Torrent Suite Software, an integrated environment to manage sequencing instrument runs and the resulting sequencing data. It allows plan a run, monitor its progress in real time, analyse and manage data. The Torrent Suite Software is optimized for the analysis of raw data using the Torrent Variant Caller plug-in, which, for example, calls single- and multi-nucleotide polymorphisms, insertions and deletions in a sample across a reference or within a subset of that reference.

More information on the data analysis workflow can be found here.

Ion Reporter Software

The Torrent Suite Software also integrates with the Ion Reporter Software, a cloud-based toolbox that helps to streamline data sharing and analysis. It automates transfer of sequencing data to the cloud, analysis and identification of variants, annotation of variants from > 20 public databases or custom annotations, reporting and archiving of sequencing data. Results can be exported in variety of formats, including summary reports, spreadsheets or plain text.

More information on Ion Reporter software analysis workflow can be found here.

Best practice analysis

Currently NGI provides best practice analysis for following applications:

  • Ion AmpliSeq Whole Transcriptome (Human/Mouse)
  • Ion AmpliSeq Whole Exome (Human)
  • Ion AmpliSeq Community Panels (Human)

Last Updated: 24th March 2022

Please read our sample submission instructions before sending samples:

Sample Submission Guidelines
Method Status


We are routinely running this method. Please visit the Order Portal to place an order.

Software tool versions

View all software versions

Compatible Methods