« Back to News

Real Time Genomics Adds Ion Torrent Support to RTG Investigator™

Ion PGM™ sequencer users can now deploy comprehensive variant and metagenomic analysis pipelines with the fastest time to results for deep genomic analysis.

October 13, 2011

SAN FRANCISCO, California, October 13, 2011 --  Real Time Genomics, Inc., today announced the immediate availability of RTG Investigator v2.3 sequence analysis software featuring native support for the Ion Torrent semiconductor sequencing platform.  With this release, Ion PGM™ users with whole genome, exome and metagenomics data can generate world class genomic analyses in minutes, using the most advanced sequence analysis software for variant detection and metagenomic analysis.

Ion PGM sequencing instruments target research and clinical applications in which speed and accuracy are critical.  Users seek the fastest time to results, measured not only by delivery speed, but also accuracy and completeness.  The quick and comparatively low cost instruments from Ion Torrent demand downstream analysis software that matches these expectations.

“Our customers place a high value on analysis software that can quickly deliver excellent results.  Real Time Genomics has created excellent sequence analysis software, and we are excited to have them extend their capabilities to the Ion Torrent platform,” said Mike Lelivelt, Director of Bioinformatics at Ion Torrent.  “RTG Investigator not only provides a robust alternative for variant detection, but opens up new opportunities for metagenomic analysis on the Ion PGM platform.”

RTG Investigator exceeds expectations by offering an efficient and comprehensive solution for deep genomic analysis that is built on a foundation of unparalleled speed and sensitivity in sequence search.  Streamlined analysis pipelines integrate the many functions required for delivery of comprehensive, accurate results into simple, consistent commands.  These pipelines are both easy to install and use, and operate much more quickly than open source alternatives.  The RTG Investigator sequence analysis platform currently delivers the fastest time to results in variant and metagenomic analysis with Illumina, Complete Genomics and Roche 454 data sets.  Now, the platform has been extended to support Ion Torrent sequence data as a native format.

“With the introduction of the Ion PGM sequencer this year, Ion Torrent is pushing next generation sequencing to a new level,” said Phillip Whalen, CEO of Real Time Genomics.  “Over the last several years, RTG has significantly advanced variant detection and metagenomic analysis for the leading NGS providers.  The combination of the Ion PGM sequencer with RTG Investigator analysis software will be unmatched for time to results.”

RTG Investigator leadership in time to results matches perfectly with analysis requirements in Ion PGM benchtop sequencing applications.  Under testing, both variant detection and metagenomic analysis pipelines were validated with Ion Torrent data from human and microbial subjects, and shown to uncover valuable insight for clinical investigation.  In both cases, initial software installation and learning curve takes one day, and analysis runs are completed in minutes.  The results of the above analyses are available in this technical brief – “Processing Ion Torrent Data Using RTG Investigator.”

Specifically, Ion Torrent amplicon data for the cystic fibrosis transmembrane conductance regulator (CFTR) gene was mapped and processed with the Bayesian SNP caller in the RTG Investigator variant detection pipeline, which quickly validated discovery of SNPs against data reported by the equivalent Ion Torrent-provided pipeline.  Over 167,000 reads were mapped in 11 seconds, with coverage ranging from 500 to 3,000x over the CFTR.21.420s region.

Similarly, the species module of the RTG Investigator metagenomic analysis pipeline was applied to data from the outbreak of Shiga-toxin producing E. coli that began in Germany, May 2011.  Ion Torrent sequence reads from the TY2482 (O104:H4) data set were mapped to a database of 1,300 bacterial species, which generated immediate insight into potential sequence component inheritance.  With this positive result, Real Time Genomics is seeking motivated investigators to collaborate on a project that further pushes the limits of the Ion PGM instrument in metagenomics.   The intent is to quickly complete a well-defined project that delivers publishable results, and provides evidence that Ion PGM can be used effectively in clinical metagenomics.  Brian Hilbush, Technical Director at Real Time Genomics, is leading this investigation.

RTG Investigator is available free to biological investigators and bioinformaticists for individual use.  Any one starting a new project can get an immediate jump-start on pipeline development. Researchers with existing pipelines can easily apply the additional sensitivity of RTG Investigator to extract premium value from current experiments or unblock investigations that require deeper analysis than existing tools can provide. Register for a free download at

Real Time Genomics ( offers easy-to-operate sequence analysis software that delivers to genome center standards. Patented and patent-pending algorithms provide unparalleled speed and sensitivity for variant detection and metagenomic analysis with Ion Torrent, Illumina, Complete Genomics and Roche 454 data sets.  Real Time Genomics is a private, San Francisco based company.

« Back to News