Abstract
A fast genome sequence aligner is proposed in this paper. The alignment algorithm is based on minimal perfect hash, reducing the memory occupation and improving memory access efficiency. Several strategies and techniques are adopted to improve the speed and accuracy of the aligner. Realized with a field programmable gate array (FPGA) based heterogeneous computing platform, the aligner achieves similar accuracy compared with BWA-MEM while the speed is around 10 times faster than BWA-MEM.
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Huang, K. et al. (2018). A Fast Genome Sequence Aligner Based on Minimal Perfect Hash Algorithm Realized with FPGA Based Heterogeneous Computing Platform. In: Zhang, F., Cai, Z., Skums, P., Zhang, S. (eds) Bioinformatics Research and Applications. ISBRA 2018. Lecture Notes in Computer Science(), vol 10847. Springer, Cham. https://doi.org/10.1007/978-3-319-94968-0_21
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DOI: https://doi.org/10.1007/978-3-319-94968-0_21
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