China’s sequencing powerhouse BGI-Shenzhen has agreed to buy the financially troubled next generation sequencing company Complete Genomics for $117.6 million or $3.15 a share, a 54 percent premium over the closing price of Complete Genomics the day prior to the California company’s June announcement that it was seeking strategic alternatives.

The Mountain View, California-based company, which has been working to provide whole genome sequencing through a service-based business model, announced a restructuring in June that included the termination of 55 employees. The company said that it was running out of cash and needed to explore strategic alternatives. At that time, it had less than six months of cash and an accumulated deficit of $250.3 million. It retained Jefferies & Company as a financial advisor and decided one option it would consider would be a merger.

Cliff Reid, chairman and CEO of Complete Genomics, said the BGI deal represented the alternative, providing stockholders with “liquidity and a premium value.” It also offers what Reid called a “great outcome for our customers, present and future.”

“The combination of the companies’ resources provides an opportunity to accelerate our vision of providing researchers and physicians with the genomic information needed to prevent, diagnose, and treat cancers and other genetic diseases,” Reid says.

As part of the deal, Complete and an affiliate of BGI have entered into an agreement pursuant to which Complete will be provided with up to $30 million in bridge financing for its operations following the signing of the merger agreement. Complete will continue to be operated as a separate company with headquarters and operations remaining in Mountain View. The transaction is expected to be completed in early 2013.

Complete provides whole human genome sequencing, which is used by research centers to conduct medical research. As part of its restructuring announcement, the company said it planned to focus on clinical applications for its whole genome scanning. BGI operates international genome sequencing centers around the world including the United States to support researchers. The companies said the combination brings together complementary scientific and technological expertise and R&D capabilities.

“Complete has developed a proprietary whole human genome sequencing technology that, together with other sequencing platforms used by BGI, will fit well with our research and business requirements and position Complete to become an even more successful global innovator,” says Wang Jun, CEO of BGI. “We look forward to growing the business to improve medical research and, when clinical services are provided, support better disease diagnosis with tools that can be used by doctors and hospitals to treat their patients.”

Once the merger is consummated, Complete will become a “key U.S. subsidiary of BGI, with the financial resources to move forward with continued development and commercialization of its whole human genome sequencing services,” said BGI in a statement to Complete’s remaining employees. “BGI intends to preserve and support Complete’s culture and maintain headquarters and operations here in Mountain View.”