Simplify your bioinformatics path to research results

Ion Reporter™ Solutions help remove the barriers of NGS data analysis, from human variant detection to microbial diversity.

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With preloaded demo research datasets for human exome, 16S metagenomics, and more, it’s simple to try Ion Reporter™ Software for yourself.  Simply log in to your account to access the cloud-based Ion Reporter™ Software.
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What's new with Ion Reporter™ Software?

Video: Ion Reporter™ solutions are ever-evolving to help meet the challenges of NGS data analysis. Dr. Carl Dowds, Sr. Product Manager of Informatics Applications, talks about the latest version of Ion Reporter™ Software and what it offers.

View video ›

Ion Reporter™ Software provides an optimized suite of simple data analysis tools that streamline Ion PGM™ and Ion Proton™ System data analysis, so you can focus on finding the biological meaning of your data.

Easy data analysis across a variety of research applications

  • Simplify your data analysis with easy-to-use preconfigured and customizable workflows, providing flexibility for users of any experience level.
  • Easily identify relevant variants with annotations from >20 public databases.

Fast results with automated workflows

  • Quickly focus on your variants of interest with simple result filtering. Then save your filter settings for standardized workflows.
  • Optimized workflows help accelerate your time to research results for Ion AmpliSeq™ targeted gene panels so you can go from sample to variants in a single day.

Security for your data

  • Control access with role-based logins, locked workflows, and audit logs to help maintain a traceable and secure environment.
  • Analyze and securely share data in the cloud, or analyze and store data on-site with the local Ion Reporter™ Server System.

Ion Reporter™ Data Analysis Workflow

1 Import
Ion Reporter Software

Automatically transfer your sequencing data from the Ion PGM™ and Ion Proton™ Torrent Servers to the cloud or local Ion Reporter™ Server using the Ion Reporter™ Uploader plugin.

2 Analyze
annotated variants for SNPs, indels, and CNVs

Use preconfigured workflows optimized for a variety of Ion AmpliSeq™ panels, or create a custom workflow to identify variants such as SNPs, indels, CNVs, and gene fusions.

3 Annotate & Filter
Ingenuity Variant Analysis

Richly annotate your variants from >20 public databases, or upload your own custom annotations and then filter for functional and biological relevance to focus on your variants of interest.

4 Visualize


Visualize variants in IGV, or easily compare variants across samples with a variety of interactive variant heat map or Venn diagram options.

View examples:
Variant impact heat map ›

Krona chart for 16S metagenomics workflows ›

Venn diagram ›

5 Report/Export

Select relevant variants and create interpretive research reports, or export variants to spreadsheet, VCF, or text format for further investigation. Also, identify complementary CE and TaqMan® Assays for variants of interest.

Single or Paired Sample Analysis

Identify differences between a single sample and a reference genome, or explore differences between variants in sample pairs.

Inherited Disease Trio Analysis

Explore variants within a pedigree.

View application note ›

Aneuploidy Analysis

Detect aneuploidies and large chromosome abnormalities from single whole-genome samples with low coverage.
Learn more ›

Gene Fusion Analysis

Detect and annotate known and novel gene fusions for the Ion AmpliSeq™ RNA Lung Fusion Panel.
Learn more ›

Tumor-Normal Comparison Analysis

Identify somatic mutations using advanced statistical approaches.

Copy Number Variation Analysis

Identify copy number variations (CNV) automatically in Ion AmpliSeq™ workflows.
Learn more ›

Annotate only (no analysis)

Upload an existing VCF and quickly identify biologically relevant variants using annotations from >20 public databases.

16S Metagenomics Analysis

Determine the microbial diversity in one or more 16S samples using reference content from MicroSEQ® DB and GreenGenes.
Learn more ›

Ion Reporter™ Server System

The Ion Reporter™ Server System combines the ease of use of Ion Reporter™ Software with the control and access of a powerful computer server in your own building.

  • Maintain a secure environment with controlled, local access on a server designed to the same robust data security standards as are described in the HIPAA rules, standards, and implementation guides
  • Control software versions and update on your timeline
  • Accelerate your clinical research with fast upload and analysis times
  • Access the same software and workflows as offered in the cloud version

View Ion Reporter™ Server flyer ›


Archive data with 20 TB of usable storage

Ion chip Storage capacity (# runs)
Ion 314™ Chip 20,000
Ion 316™ Chip 10,000
Ion 318™ Chip 4,000
Ion PI™ Chip 400
Ion PII™ Chip* 200
Number of Ion PGM™ and Ion Proton™ Sequencer runs that can be stored on the Ion Reporter™ Server. Assumes file footprint sizes of 1 GB (Ion 314™ Chip), 2 GB (Ion 316™ Chip), 5 GB (Ion 318™ Chip), 50 GB (Ion PI™ Chip), and 100 GB (Ion PII™ Chip*).

Find your biological meaning fast

Examples of analysis run times on the Ion Reporter™ Server for annotating an exome-size VCF (variant call format) file, to running a complete analysis on various sized Ion AmpliSeq™ panels. Mapping: the alignment of the raw reads back to a reference genome; Variant Calls: the identification of variants when compared to a reference genome; Stats: the generation of mapping, coverage, and QC stats; Annotation: the notation of identified variants using a rich set of public sources. Analysis run times represent tens of variants for the Ion AmpliSeq™ Cancer Hotspot Panel v2, thousands of variants for the Ion AmpliSeq™ Comprehensive Cancer Panel, and tens of thousands of variants for the Ion AmpliSeq™ Exome Panel.

Partek® Flow® software on the Ion Reporter™ Server

In addition to the Ion Reporter™ Software, the Ion Reporter™ Server System can also host third-party Partek® Flow® software for RNA-Seq data analysis.  Hosted side by side with the Ion Reporter™ software, Partek® Flow® software enables simple RNA-Seq data analysis with preconfigured, Ion Torrent™-validated whole-transcriptome and small-RNA data analysis pipeline optimized for Ion Proton™ sequencing data.

Learn more about Partek® Flow® software and transcriptome sequencing ›

Note: Hosted Data Storage includes cloud-based Ion Reporter™ Software data analysis and storage.