Reconfigurable acceleration of genetic sequence alignment: A survey of two decades of efforts

Ho-Cheung Ng, Shuanglong Liu, Wayne Luk
2017 2017 27th International Conference on Field Programmable Logic and Applications (FPL)  
Genetic sequence alignment has always been a computational challenge in bioinformatics. Depending on the problem size, software-based aligners can take multiple CPUdays to process the sequence data, creating a bottleneck point in bioinformatic analysis flow. Reconfigurable accelerator can achieve high performance for such computation by providing massive parallelism, but at the expense of programming flexibility and thus has not been commensurately used by practitioners. Therefore, this paper
more » ... ms to provide a thorough survey of the proposed accelerators by giving a qualitative categorization based on their algorithms and speedup. A comprehensive comparison between work is also presented so as to guide selection for biologist, and to provide insight on future research direction for FPGA scientists.
doi:10.23919/fpl.2017.8056838 dblp:conf/fpl/NgLL17 fatcat:3nqeo75ysbfdrar2qx75yvw3ba