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Ion Torrent Prepares to Launch Cloud-based Variant Analysis Software by Mid-Year


By Uduak Grace Thomas

Ion Torrent is set to become the latest sequencing vendor to dip its toes into the commercial bioinformatics arena.

The Life Technologies subsidiary said this week that it plans to launch a commercial cloud-based variant analysis software package, dubbed Ion Reporter, in the first half of this year.

Ion Reporter, which will operate under a software-as-a-service model, will include open source algorithms that the company has developed for calling genetic variants, Alan Willliams, Ion Torrent's vice president of software and informatics, told BioInform.

While the company previously released some open source algorithms that are used in its Torrent Suite software, Ion Reporter will be the first "Ion branded" commercial software package to be offered as a standalone product, Williams said.

The suite, which runs on the Torrent Server, includes algorithms for base calling; a tool called T-MAP that is used for mapping and aligning Ion Torrent sequence data; as well as algorithms for calling variants including SNPs, insertions, and deletions, he said.

While it is likely that certain capabilities in Ion Reporter will compete with offerings from some vendors in Ion Torrent's partner program, among other pure-play bioinformatics vendors, the tool will target particular segments of the market, thereby leaving enough room for "multiple players," Williams said.

For instance, Ion Reporter's software-as-a-service model may not work for customers who have particular policies in place that govern data handling. Furthermore, the tool is specifically intended for customers looking for variants in human data, he said.

The launch is part of the company's broader business strategy for playing in the next-generation sequencing space, which is to "enable complete solutions that include kits and reagents and chips and software for particular applications," Williams said.

"The reality is that there are so many broad applications based on next-gen sequencing technologies, that it's more important that we work with a number of both reagent vendors and software developers to make sure that there is a fairly broad variety of solutions out there," he said.

For the time being, the company is keeping many of the details about its new software offering under wraps. For example, it isn't releasing information about the cloud provider selected to host Ion Reporter. Nor is it providing any pricing information, though BioInform's sister publication In Sequence reported this week that the tool will have a pay-per-use fee associated with it (IS 1/10/2012).

Willliams told BioInform that the tool is currently being tested by five unnamed early-access customers.

When it is released, Ion Reporter will be capable of handling data from both Ion Torrent's Personal Genome Machine and the Ion Proton sequencer, a new instrument that promises to sequence a human genome in a day for under $1,000 that the company plans to launch by mid-2012.

Both platforms will include an option to stream data automatically from the sequencer to the cloud for further analysis using Ion Reporter via the Torrent Server, he said.

When it launches Ion Reporter, Ion Torrent will officially join the roster of sequencing instrument vendors that are branching out into the bioinformatics software market.

Last October, Illumina launched a cloud-based analysis offering dubbed BaseSpace to provide free data-management, archiving, analysis, and storage tools for users of its MiSeq personal sequencer system, adding that it planned to extend the tool to support data from other sequencers (BI 10/14/2011).

In April, Pacific Biosciences launched an open source software suite to provide secondary analysis for its PacBio RS single-molecule sequencing system and then announced a partnership with Cycle Computing in September to provide a cloud-version of the tool (BI 9/29/2011).

Similarly, in May, Ion Torrent's parent company, Life Technologies began offers a cloud-based option for its LifeScope Genomics analysis software for its 5500 SOLiD sequencer (BI 5/27/2011).

Have topics you'd like to see covered in BioInform? Contact the editor at uthomas [at] genomeweb [.] com.