SeqHive: A Reconfigurable Computer Cluster for Genome Re-sequencing

We demonstrate how Field Programmable Gate Arrays (FPGAs) may be used to address the computing challenges associated with assembling genome sequences from recent ultra-high-throughput sequencing technologies. Advances in sequencing technology allow researchers to generate immense amounts of raw data in the form of short reads with high error rates. A prerequisite to effectively utilizing this data for most applications is accurate alignment to a reference genome. While dynamic programming (DP) alignment algorithms are generally avoided on conventional architectures due to their computational complexity, they can be tailored for efficient implementation on systolic architectures. We describe and implement the first system capable of assembling large genomes using DP. We implemented application-specific DP algorithms for aligning data from ultra-high-throughput sequencers in a reconfigurable computing cluster. To obtain the necessary throughput while maintaining scoring integrity, we ext...

• Type: Journal
• Year: 2010
• Where: FPL
• Authors: Kristian Stevens, Henry Chen, Terry Filiba, Peter McMahon, Yun S. Song
• Keywords: Error Rates, FPL 2010, Hardware, Programmable Gate Arrays, Reference Genome