Research applications

Ion Reporter™ Software supports research applications to use when setting up analysis workflows. The research application selections work with sample group selections, and affect the options that are available in subsequent workflow steps.

The default options are recommended as best practice, but advanced users can adjust the recommended settings, if necessary.

Research application



Detect human chromosomal large structural abnormalities in low-pass whole-genome sequencing research samples.

Annotate Variants

Annotate the variants from a VCF file for research use.


Detect and annotate variants in human DNA research samples.

DNA and Fusions

Detect and annotate variants in human DNA and fusions research samples.

Immune Repertoire [1]

Detect and analyze T cell receptor beta (TCRB) rearrangements for research use.


Determine population diversity in polymicrobial research samples using detection of 16S gene variable regions.

Mutation Load 1

Calculates mutation load and displays associated graphs and tables in human DNA samples.

Note: This research application applies only to the Oncomine™ Tumor Mutation Load - w1.0 - DNA - Single Sample analysis workflow that was released with Ion Reporter™ Software 5.6.

Oncology-Liquid Biopsy1

Detects and annotates low frequency variants including SNPs and INDELs (down to 0.1% limit of detection), Fusions, and CNVs from targeted nucleic acid libraries (DNA or RNA).


Detect and annotate gene fusions in human DNA research samples.


This research application is for use only with a copy and edit of an analysis workflow. This research application is not an option when you create a custom analysis without predefined settings.