Prognosys Biosciences, a La Jolla, Calif.-based sequencing services vendor, has jumped on the next-generation sequencing data-analysis bandwagon with the launch of a cloud platform that provides bioinformatics pipelines specifically for RNA-seq data.
While the company has offered data analysis to customers as part of its sequencing services package, the RNA-seq pipeline — dubbed Voila! — is its first standalone bioinformatics product.
Jill Dombrauckas, Prognosys's director of marketing, told BioInform that the company launched the platform to meet demand in the market for data analysis and management tools as well as to provide a single source for customers to access sequencing services and analysis tools.
She explained that when Prognosys opened its doors in 2004, it initially focused on providing next-generation sequencing services at a time when the technology was novel.
The company's sequencing services arm, called Sequencys, offers DNA resequencing, de novo sequencing, and RNA sequencing services using Illumina's TruSeq technology. It also offers target-enrichment kits and services based on its proprietary technology.
However, as NGS has become more prevalent and cheaper, Prognosys has turned its attention toward improving its data-analysis tools and is now making them available to customers who lack the "appropriate expertise" to analyze the data, Dombraukas said.
Built on Amazon's EC2 cloud infrastructure, Voila! accepts data from Illumina’s HiSeq and Genome Analyzer platforms and uses a combination of open source and proprietary algorithms that have been optimized to run on the Prognosys cloud.
Customers can use the platform to analyze data on gene expression, exons, splice junctions, and variant calling and receive the results of the analysis in annotated tables that can be further analyzed by standard statistical packages.
The system also includes tools for data quality control and to generate project quotes based on the number of samples that need to be analyzed. Furthermore, customers receive three months of storage with an option to extend that time frame if they need to.
Introductory pricing for the analysis starts at $79 per sample for up to 50 million reads.
Prognosys chose to focus the cloud offering on RNA-seq because it’s the most "complex and challenging" data to analyze, Dombrauckas said, adding that the company has also developed tools that it uses internally for analyzing whole-genome and targeted sequencing data.
Prognosys plans to move all of its analysis tools to the cloud eventually, but it wanted to ensure that its cloud platform could run the RNA-seq pipeline smoothly first.
"As soon as we have established that, we can load the other tools in as well," Dombrauckas said, although she could not provide a target release date.
Furthermore, Prognosys plans to tweak its analysis pipeline to handle data from other sequencing platforms besides Illumina's, though the specific development roadmap will depend in part on customer requests.
In the marketplace, Voila! will compete with companies like DNAnexus that also provide cloud services as well as products from software vendors for RNA-seq analysis.
Moreover, Prognosys also has to contend with instrument manufacturers like Illumina who have released analysis software tailored to handle data from their sequencing instruments.
However, competing platforms like the DNAnexus cloud, for example, are focused on visualizing results, Dombrauckas said, while Prognosys has adopted the "opposite approach," choosing to focus instead on extracting "valuable information" from customers' data.
For example, she noted that the DNAnexus cloud-based analysis service doesn’t provide tools for calling de novo exons or for analyzing splice junctions, both of which are included in Voila!.
Furthermore, the cloud-based model means that customers get new tool updates faster and don’t have to purchase a new version of the software when there are upgrades, she pointed out.
Besides its sequencing and data analysis businesses, Prognosys also offers assay development and is involved in biomarker discovery and diagnostics efforts. Its tools and technologies are currently being used in several NIH-funded genomics and proteomics projects.
Furthermore, Prognosys also offers custom target enrichment kits, which use solution-based hybridization to capture defined regions of the genome, as a product and a service for human, mouse, and rat genomes.
Have topics you'd like to see covered in BioInform? Contact the editor at uthomas [at] genomeweb [.] com