Abstract
Next generation DNA sequencing machines have been improving at an exceptional rate; the subsequent analysis of the generated sequenced data has become a bottleneck in current systems. This paper explores the use of reconfigurable hardware to accelerate the short read mapping problem, where the positions of millions of short DNA sequences are located relative to a known reference sequence. The proposed design comprises of an alignment processor based on a backtracking variation of the FM-index algorithm. The design represents a full solution to the short read mapping problem, capable of efficient exact and approximate alignment. We use reconfigurable hardware to accelerate the design and find that an implementation targeting the MaxWorkstation performs considerably faster and more energy efficient than current CPU and GPU based software aligners.
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References
Ferragina, P., Manzini, G.: An experimental study of an opportunistic index. In: ACM-SIAM Symposium on Discrete Algorithms (SODA 2001), pp. 269–278 (2001)
Langmead, B., et al.: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10(3), R25+ (2009)
Li, R., et al.: SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25(15), 1966–1967 (2009)
Burrows, M., Wheeler, D.: A block-sorting lossless data compression algorithm. Digital Equipment Corporation, Tech. Rep. (1994)
Fernandez, E., Najjar, W., Lonardi, S.: String matching in hardware using the FM-index. In: Proc. FCCM, pp. 218–225 (2011)
Preuer, T.B., Knodel, O., Spallek, R.G.: Short-read mapping by a systolic custom FPGA computation. In: Proc. FCCM, pp. 169–176 (2012)
Tang, W., et al.: Accelerating millions of short reads mapping on a heterogeneous architecture with FPGA accelerator. In: Proc. FCCM, pp. 184–187 (2012)
Olson, C.B., et al.: Hardware acceleration of short read mapping. In: Proc. FCCM, pp. 161–168 (2012)
Lam, T., Li, R., Tam, A., Wong, S., Wu, E., Yiu, S.: High throughput short read alignment via bi-directional bwt. In: IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 31–36 (November 2009)
Li, H., Durbin, R.: Fast and accurate short read alignment with burrows wheeler transform. Bioinformatics 25(14), 1754–1760 (2009)
Liu, C.-M., et al.: SOAP3: Ultra-fast GPU-based parallel alignment tool for short reads. Bioinformatics 28(6), 878–879 (2012)
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Arram, J., Tsoi, K.H., Luk, W., Jiang, P. (2013). Hardware Acceleration of Genetic Sequence Alignment. In: Brisk, P., de Figueiredo Coutinho, J.G., Diniz, P.C. (eds) Reconfigurable Computing: Architectures, Tools and Applications. ARC 2013. Lecture Notes in Computer Science, vol 7806. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-36812-7_2
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DOI: https://doi.org/10.1007/978-3-642-36812-7_2
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-36811-0
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