NEW YORK (GenomeWeb) – Earlier this month, the National Center for Genome Resources (NCGR), a nonprofit research institute, and Simbiot, a bioinformatics firm, jointly launched Lumenogix NGS, an informatics platform for managing and analyzing next-generation sequence data.
The platform is developed and sold by Lumenogix, a company that NCGR and Simbiot formed to commercialize technology they had both developed internally. Specifically, the company officially opened its doors in January and licensed from Simbiot capabilities for handling large complex NGS datasets, Boris Umylny, CEO of Simbiot and Lumenogix, told BioInform.
Simbiot previously sold a software-as-a-service platform that offered applications for managing and analyzing NGS data. Lumenogix NGS also incorporates analysis algorithms developed and used within NCGR, and it features a researcher-friendly user interface designed within NCGR to provide access to its constituent tools, Umylny said.
Lumenogix NGS has algorithms for read mapping, variant analysis, data visualization, and more. These algorithms have been bundled into various analysis pipelines for analyzing RNA-seq data, ChIP-seq data, and microRNA-seq data. Also available are two mutation identification pipelines, one of which is used to identify SNPs and short insertions and deletions, and the other to call longer indels. Lumenogix is working on additional pipelines for its platform, Umylny said, including one for identifying copy number variants. Also available are tools to track samples during analysis and securely share large datasets as part of collaborative research projects, as well as applications to mine data from public repositories.
Lumenogix targets Lumenogix NGS at researchers in academia and industry, and offers the product in three configurations. In the first option, researchers access the resource remotely on a private cloud maintained and run by NCGR. Alternatively, researchers who prefer to keep their work local can have the system installed on internal servers. A third option is to install the Lumenogix NGS appliance, which provides customers with a turnkey solution that includes both hardware and software.
Lumenogix has adopted a per-user pricing model that applies no matter which configuration a user chooses to install. The company isn't disclosing the exact amount that it charges publicly but it believes that its pricing is competitive when compared to similar software in the market. Umylny said that the company has compared the cost of processing data on the Lumenogix appliance to the cost of trusting the analysis to a service provider or analyzing it using infrastructure from current cloud vendors.
Depending on the service provider, the cost of analyzing an exome, for instance, generally falls between $60 and $250 per sample, he said. Doing the analysis on the cloud is cheaper, only about $30 per sample, but researchers have to pay for storage, which adds to the final price tag. Running the same analysis on the Lumenogix appliance comes to about $16 per sample, he said. Furthermore, the appliance comes with 60 terabytes of storage space, helping researchers save on storage costs.
Competitive cost is one factor that will help Lumenogix compete in what is a very crowded marketplace that includes players like CLC Bio — now owned by Qiagen — and DNAnexus, but where the company really stands out, Umylny said, is in the quality of the software it sells and the service that it provides.
"The system that we have is so efficient in terms of processing the data that we can actually offer lower cost and better service and still make money in the process," he told BioInform. Also, unlike some competitors who sell their systems and leave the customers to figure out how to use it, "we provide constant support to our users." That's especially important for clients who aren't bioinformatics experts and who may be daunted by the kind of detailed documentation some companies provide, he added.
With the launch of Lumenogix and its NGS platform, Simbiot no longer sells its SaaS offering. The company continues to exist and holds the license to the technology that underlies Lumenogix NGS but all of its customers are now Lumenogix clients and the Simbiot sales team is focused on peddling the newer platform in the market place, Umylny said. It's not clear if Simbiot will eventually be subsumed by Lumenogix. Decisions about the corporate structure of both companies will be made further down the road, Umylny said, "Right now we are focusing on developing the best most effective platform around and successfully marketing it."
Current customers of Lumenogix NGS include NCGR and the University of New Mexico, as well as some unnamed biotechnology companies based in San Diego. The tool is being used to analyze data from infectious disease and antibody-analysis projects, among other uses, Umylny said.