Accelerating Metagenomics Using Graphics Processing Units

A key application of the technological breakthrough associated with decreased cost of DNA sequencing is metagenomics. Metagenomics is the process of sequencing DNA from whole ecosystems, rather than individuals or cultures. This approach has the potential to allow the dissection of microbial ecosystems in biofuel producing agricultural land, toxic contaminated sites and hydrocarbon recovery environments, and as such is of substantial and recognized importance to DoE. The limiting technology for metagenomics is currently the huge amounts of computer power needed to process sequences and determine their origin. The overall objective of this proposal is to develop software for metagenomic sequence analysis which takes advantage of the computing power of graphics processing units (GPUs) using CUDA, a programming interface allowing rapid development of software which utilizes the processing power of the GPU for applications other than graphics. Commercial Applications and Other Benefits: The advantage of sequence analysis software which runs on GPUs is that it will run at much higher speeds than currently available on inexpensive computer hardware. By making this software commercially available we will produce a product which will make DNA sequence analysis much more affordable, both for metagenomics and other applications.