Hardware accelerated alignment algorithm for optical labeled genomes

ACM Transactions on Reconfigurable Technology and Systems

Volumn 9, Issue 3, 2016, Pages

  Meng, Pingfan ^a   Jacobsen, Matthew ^a   Kimura, Motoki ^a   Dergachev, Vladimir ^b   Anantharaman, Thomas ^b   Requa, Michael ^b   Kastner, Ryan ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b USA   (United States)

Author keywords

Acceleration; De novo assembly; FPGA; Genome; GPU

Indexed keywords

ACCELERATION; BIOINFORMATICS; FIELD PROGRAMMABLE GATE ARRAYS (FPGA); INTEGRATED CIRCUIT DESIGN; OPTIMIZATION; RECONFIGURABLE HARDWARE;

ALIGNMENT ALGORITHMS; ASSEMBLY ALGORITHM; DE NOVO ASSEMBLIES; DESIGN SPACE EXPLORATION; HARDWARE-ACCELERATED; LARGE SCALE STRUCTURES; OPTIMIZATION TECHNIQUES; SEQUENTIAL SOFTWARES;

GENES;

EID: 84988409362     PISSN: 19367406     EISSN: 19367414     Source Type: Journal    
DOI: 10.1145/2840811     Document Type: Article

References (14)

1. A. M. Aji, L. Zhang, and W. C. Feng. 2010. GPU-RMAP: Accelerating short-read mapping on graphics processors. In 2010 IEEE 13th International Conference on Computational Science and Engineering (CSE'10). 168-175. DOI:http://dx.doi.org/10.1109/CSE.2010.29
2. M. Baday, A. Cravens, A. Hastie, H. J. Kim, D. E. Kudeki, P.-Y. Kwok, M. Xiao, and P. R. Selvin. 2012. Multicolor super-resolution DNA imaging for genetic analysis. Nano Letters 12, 7 (2012), 3861-3866.
3. I. Birol, S. D. Jackman, C. B. Nielsen, J. Q. Qian, R. Varhol, G. Stazyk, R. D. Morin, Y. Zhao, M. Hirst, J. E. Schein, D. E. Horsman, J. M. Connors, R. D. Gascoyne, M. A. Marra, and S. J. M. Jones. 2009. De novo transcriptome assembly with ABySS. Bioinformatics 25, 21 (2009), 2872-2877. DOI:http://dx.doi.org/10.1093/bioinformatics/btp367
4. A. R. Hastie, L. Dong, A. Smith, J. Finklestein, E. T. Lam, N. Huo, H. Cao, P.-Y. Kwok, K. R. Deal, J. Dvorak, M.-C. Luo, Y. Gu, and M. Xiao. 2013. Rapid genome mapping in nanochannel arrays for highly complete and accurate De Novo sequence assembly of the complex Aegilops tauschii genome. PLoS ONE 8, 2 (02 2013), e55864. DOI:http://dx.doi.org/10.1371/journal.pone.0055864
5. M. Jacobsen and R. Kastner. 2013. RIFFA 2.0: A reusable integration framework for FPGA accelerators. In 2013 23rd International Conference on Field Programmable Logic and Applications (FPL'13). 1-8. DOI:http://dx.doi.org/10.1109/FPL.2013.6645504
6. E. T. Lam, A. Hastie, C. Lin, D. Ehrlich, S. K. Das, M. D. Austin, P. Deshpande, H. Cao, N. Nagarajan, M. Xiao, and P.-Y. Kwok. 2012. Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly. Nature Biotechnology 30, 8 (2012), 771-776.
7. C.-M. Liu, T. Wong, E. Wu, R. Luo, S.-M. Yiu, Y. Li, B. Wang, C. Yu, X. Chu, K. Zhao, R. Li, and T.-W. Lam. 2012. SOAP3: Ultra-fast GPU-based parallel alignment tool for short reads. Bioinformatics 28, 6 (2012), 878-879. DOI:http://dx.doi.org/10.1093/bioinformatics/bts061
8. P. Meng, M. Jacobsen, M. Kimura, V. Dergachev, T. Anantharaman, M. Requa, and R. Kastner. 2014. Hardware accelerated novel optical de novo assembly for large-scale genomes. In 2014 24th International Conference on Field Programmable Logic and Applications (FPL'14). 1-8. DOI:http://dx.doi.org/10.1109/FPL.2014.6927499
9. C. B. Olson, M. Kim, C. Clauson, B. Kogon, C. Ebeling, S. Hauck, and W. L. Ruzzo. 2012. Hardware acceleration of short read mapping. In 2012 IEEE 20th Annual International Symposium on Field-Programmable Custom Computing Machines (FCCM'12). 161-168. DOI:http://dx.doi.org/10.1109/FCCM.2012.36
10. A. Valouev. 2006. Shotgun Optical Mapping: A Comprehensive Statistical and Computational Analysis. Ph.D. Dissertation. Los Angeles, CA. Advisor(s) Waterman, Michael.
11. B. S. C. Varma, K. Paul, and M. Balakrishnan. 2014. Accelerating genome assembly using hard embedded blocks in FPGAs. In 2014 27th International Conference on VLSI Design and 2014 13th International Conference on Embedded Systems. 306-311. DOI:http://dx.doi.org/10.1109/VLSID.2014.59
12. B. S. C. Varma, K. Paul, M. Balakrishnan, and D. Lavenier. 2013. FAssem: FPGA based acceleration of de novo genome assembly. In 2013 IEEE 21st Annual International Symposium on Field-Programmable Custom Computing Machines (FCCM'13). IEEE Computer Society, 173-176. DOI:http://dx.doi.org/10.1109/FCCM.2013.25
13. Xilinx. 2014. Xilinx Products. http://www.xilinx.com/products/boards-and-kits/ek-v7-vc707-g.html. (2014). [Online].
14. A. Zuccolo, A. Sebastian, J. Talag, Y. Yu, H.-R. Kim, K. Collura, D. Kudrna, and R. A. Wing. 2007. Transposable element distribution, abundance and roleingenome size variationinthe genus oryza. BMC Evolutionary Biology 7, 1 (2007), 152.