Accelerating Phylogeny-Aware Short DNA Read Alignment with FPGAs

• Published in: 2011 IEEE 19th Annual International Symposium on Field-Programmable Custom Computing Machines pp. 226 - 233
• Main Authors: Alachiotis, N, Berger, S A, Stamatakis, A
• Format: Conference Proceeding
• Language: English
• Published: IEEE 01.05.2011
• Subjects: Acceleration; Computer architecture; Dynamic programming; Field programmable gate arrays; FPGA; Kernel; Microprocessors; multiple alignment; phylogenetic inference; Phylogeny
• ISBN: 9781612842776; 1612842771
• DOI: 10.1109/FCCM.2011.13

Recent advances in molecular sequencing technology have given rise to novel algorithms for simultaneously aligning short sequence reads to reference sequence alignments and corresponding evolutionary reference trees. We present a complete hardware/software implementation for the acceleration of a program called PaPaRa, a newly introduced dynamic programming algorithm for this purpose. We verify the correctness of the proposed architecture on a real FPGA and introduce a straight-forward communication protocol(using gigabit ethernet) for seamless integration with the encapsulating steering software that is executed on a PC processor. The hardware description and the software implementation are freely available for download. When mapped to a Virtex 6 FPGA, our reconfigurable architecture can compute 133.4 billion cell updates per second for the novel, tree-based alignment kernel of PaPaRa. Compared to PaPaRa, running on a 3.2GHz Intel Core i5 CPU, we obtain speedups for the alignment kernel, that range between 170 and 471. For the entire application, that is, the alignment kernel and the trace-back step, we obtain speedups between 74 and 118.