Ion Reporter Software Integration Guide

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Torrent Suite Software space on Ion Community

IR Integration TOC

Integration with Ion Reporter Software

This section provides a high level view of the phases of an Ion Reporter Software analysis and also how these phases tie in with Torrent Suite Software analyses. (This section presents a simplification and is intended to show new users how Ion Reporter Software relates to their Torrent Suite Software analyses.)

What is Ion Reporter Software?

Ion Reporter Software comprises a suite of bioinformatics tools that streamlines and simplifies the data analysis, annotation, and reporting of Ion Torrent semiconductor sequencing data. Designed for both exploratory and production use in performing sequencing assays, Ion Reporter Software helps you overcome the bioinformatics barriers to interpret DNA variants faster and more consistently. For researchers needing a simple, reproducible bioinformatics tool that helps ensure consistency in their results, Ion Reporter Software is an ideal solution.

Integrate your variants with comprehensive public and curated annotations, along with your own lab-specific content. Ion Reporter Software is designed to reduce the time-to-results. Configurable analysis modules and parameters allow customization of workflows to fit your research needs.

All the steps, from data import to annotating variants, are automated in Ion Reporter Software workflows. Key features include the following:

• Detection of SNPs, indels, and CNVs in one easy to use workflow
• Automated analysis workflows for 1, 2, or 3 samples
• Hosted and local deployment options to suit your lab's needs
• Simple interface to drive intuitive user experience
• Role-based logins and full auditability so you can tell who did what and when
• Extensive annotations to guide understanding of your sample's variants
• Flexible batch export for integration into laboratory systems and APIs in support of third-party tools for external analysis

Torrent Suite Software output

Typically the BAM file output of your Torrent Suite Software analysis is uploaded to Ion Reporter Software and then Ion Reporter Software runs through its analysis phases of mapping, variant calling, and annotation. This table shows how Torrent Suite Software output files are used in Ion Reporter Software analyses:

The Ion Reporter Uploader plugin by default uploads both the BAM file and the VCF file from your Torrent Server to Ion Reporter Software.

Ion Reporter Software analysis files

Ion Reporter Software analysis involves the following major analysis phases:

1. Mapping

2. Variant calling

3. Annotation

The following table describes the input and output file types for the analysis phases:

Each output file type is required as input to the next analysis phase. In almost all cases, the Ion Reporter Software analysis phases are performed in order.

The exception is the annotation phase. The annotation-only workflow runs this phase by itself. (All other workflows include the annotation phase as their last analysis phase.) The annotation-only workflow requires as input a VCF file, which can be generated from either a Ion Reporter Software analysis, a Torrent Suite Software Torrent Variant Caller (TVC) plugin analysis, or a different source.

File Transfer

You can configure the Ion Reporter Uploader plugin to transfer your files automatically and you can also transfer files on a completed Torrent Suite Software analysis. S ee The IonReporterUploader Plugin .

Ion Reporter Software features that relate to variant calling

For information on how Ion Reporter Software can help with your interpretation of variants, see Ion Reporter Software Features Related to Variant Calling .

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