Ion Reporter™ Software
Advancing Clinical Research
Breaking bioinformatics barriers with automated variant analysis
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Ion Reporter™ Software automates all steps of your bioinformatics pipeline
All the steps—from launching the sequencing run to annotating variants—are automated in the Ion Reporter™ Software workflow. The newest features of the software include:
- Staged versioning—allows migration of data and workflows from one release to the next on your own schedule without disrupting validated workflows
- Archive—long-term storage of data and results depending on your laboratory’s needs
- Collaboration space—share workflows, samples, analyses, and results with other individuals or organizations within consortia and core facilities
- Biomarker discovery workflows—in addition to routine reporting, new discovery tools allow you to mine your data for novel biological impacts
- Flexible batch export—integration into laboratory systems and APIs in support of third-party tools for external analysis
- Custom AmpliSeq™ designs—automatically pull your fixed panels and custom AmpliSeq™ designs from ampliseq.com into your IR workflow
Initiate analysis
Upload data—Sequence reads from Ion PGM™ or Ion Proton™ Systems are automatically uploaded from the Torrent Suite Software to the hosted Ion Reporter™ Software for automated mapping, variant detection, and annotation—all with version control and audit traceability.
Select a preconfigured workflow—The data upload step includes workflow selection, which efficiently integrates data generation on the Torrent Server with data analysis in Ion Reporter™ Software—just select the samples and an experimental design to launch the analysis.
Launch analysis—Ion Reporter™ Software is equipped with a series of standard workflows that can be further customized for most common DNA variant analyses:
 | Single Sample Analysis Find differences from sample and reference genome |  | Somatic Paired Analysis Compare variants between tumor and germline sample |
 | Paired Analysis Explore differences between variants in sample pairs |  | Inherited Disease Trio Analysis Explore variants within a family |
Ion Reporter™ Software workflows are flexible—every parameter in the workflow can be tuned to suit your particular analysis and then locked for repeated use with new data sets in a production environment.
Review variants and annotationsDefine workflows for production use—The researcher filters the identified variants based on technical criteria such as read coverage, P-value, or allele frequency. These settings can be saved and reapplied to future runs, which helps to ensure reproducibility. Ion Reporter™ Software enables you to see precisely how the reads align against the reference genome and provide evidence for the variant calls, allowing you to quickly filter variants that do not meet your lab’s technical standards or are outside the scope of your project. | 
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Interpret variants and generate reports
Classify variants by impact—Ion Reporter™ Software automatically connects publicly available genomic annotations to each identified variant, producing systematic and up-to-date annotations. Before each sequencing run, the user can choose from a list of public database annotations that are preloaded into the software (annotations are updated at every Ion Reporter™ Software release). This automated feature replaces the time-consuming data curation step required to obtain the latest annotations from multiple databases. Additionally, users can also upload their own content. In the report role, a domain expert explores and filters annotations to easily find relevant variants and interpret them.
Interpret each variant—Researchers can save and reuse interpretations on specific variants that commonly appear in their routine samples. After the relevant variants have been selected, they are classified and interpreted. This includes annotations for detected variants and custom comments that describe each variant within the context of the analysis.
Write summary report—Ion Reporter™ Software then creates an easily digestible report that displays the relevant variants and their annotations, as well as written interpretive statements and summary classifications. This interpretive report can be shared and saved for your records. The entire analysis custody chain is electronically captured, enabling rigorous access and process audits.
Manage data securely
Manage data archiving—Researchers can use Ion Reporter™ Software to manage data over the long term and to organize individual files and audit logs. Retrieve data and results—The data can be either archived on the cloud or downloaded for local storage. Ion Reporter™ Software operates using staged version migration, so users can take advantage of algorithm improvements on their own timelines without jeopardizing current production workflows.
Ingenuity® Variant Analysis™ WorkflowThe fastest way to identify biologically relevant variantsThe Ingenuity® Variant Analysis™ Workflow rapidly identifies pathogenic variants from semiconductor sequencing data and interprets their impact on signaling pathways and drug response. It enables knowledge-driven identification of disease-causing variants by leveraging the expert-curated Ingenuity® Knowledge Base™, which includes over 4 million variant and gene findings from literature and public databases. The Variant Analysis™ Workflow is integrated into Ion Reporter™ Software so you can securely transfer and analyze your data without logging in again or manually uploading files. |  |
Mike Lelivelt, PhD, Director of Bioinformatics at Ion Torrent discusses Ion Reporter Software.
Designed specifically for researchers performing routine sequencing assays.
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Phone and EmailFor Research Use Only. Not intended for any animal or human therapeutic or diagnostic use. The content provided herein may relate to products that have not been officially released and is subject to change without notice.
