GPU-accelerated bidirected De Bruijn graph construction for genome assembly

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 7808 LNCS, Issue , 2013, Pages 51-62

  Lu, Mian ^a   Luo, Qiong ^b   Wang, Bingqiang ^c   Wu, Junkai ^b   Zhao, Jiuxin ^b  

^a INSTITUTE OF HIGH PERFORMANCE COMPUTING   (Singapore)

^b HONG KONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Hong Kong)

^c BGI SHENZHEN   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DE BRUIJN GRAPHS; GENOME ASSEMBLY; GPU-ACCELERATED; GRAPH CONSTRUCTION; GRAPHICS PROCESSING UNIT; LARGE AMOUNTS; LARGE DATASETS; SECOND GENERATION;

COMPUTER GRAPHICS; COMPUTER GRAPHICS EQUIPMENT; GENES; PROGRAM PROCESSORS; SUPERCOMPUTERS;

PIPELINE PROCESSING SYSTEMS;

EID: 84875830808     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-37401-2_8     Document Type: Conference Paper

References (16)

1. Jackson, B., Regennitter, M., Yang, X., Schnable, P., Aluru, S.: Parallel de novo assembly of large genomes from high-throughput short reads. In: IPDPS 2010: Proceedings of the 2010 IEEE International Symposium on Parallel&Distributed Processing, pp. 1-10 (April 2010)
2. Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G., Kristiansen, K., Li, S., Yang, H., Wang, J., Wang, J.: De novo assembly of human genomes with massively parallel short read sequencing. Genome Research 20(2), 265-272 (2010)
3. Simpson, J.T., Wong, K., Jackman, S.D., Schein, J.E., Jones, S.J., Birol, I.: Abyss: a parallel assembler for short read sequence data. Genome Research 19(6), 1117-1123 (2009)
4. Zerbino, D.R., Birney, E.: Velvet: algorithms for de novo short read assembly using de bruijn graphs. Genome Research 18(5), 821-829 (2008)
5. Pevzner, P.A., Tang, H.: Fragment assembly with double-barreled data. Bioinformatics 17(suppl. 1), S225-S233 (2001)
6. Medvedev, P., Georgiou, K., Myers, G., Brudno, M.: Computability of models for sequence assembly. In: Giancarlo, R., Hannenhalli, S. (eds.) WABI 2007. LNCS (LNBI), vol. 4645, pp. 289-301. Springer, Heidelberg (2007)
7. Chaisson, M.J., Pevzner, P.A.: Short read fragment assembly of bacterial genomes. Genome Research 18(2), 324-330 (2008)
8. Hossain, M.S.S., Azimi, N., Skiena, S.: Crystallizing short-read assemblies around seeds. BMC Bioinformatics 10(suppl. 1) (2009)
9. Hernandez, D., François, P., Farinelli, L., Østerås, M., Schrenzel, J.: De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer. Genome Research 18(5), 802-809 (2008)
10. Butler, J., MacCallum, I., Kleber, M., Shlyakhter, I.A., Belmonte, M.K., Lander, E.S., Nusbaum, C., Jaffe, D.B.: Allpaths: De novo assembly of whole-genome shotgun microreads. Genome Research 18(5), 810-820 (2008)
11. Warren, R.L., Sutton, G.G., Jones, S.J., Holt, R.A.: Assembling millions of short dna sequences using ssake. Bioinformatics 23(4), 500-501 (2007)
12. Dohm, J.C., Lottaz, C., Borodina, T., Himmelbauer, H.: Sharcgs, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Research 17(11), 1697-1706 (2007)
13. Jackson, B.G., Aluru, S.: Parallel construction of bidirected string graphs for genome assembly. In: International Conference on Parallel Processing, pp. 346-353 (2008)
14. Kundeti, V., Rajasekaran, S., Dinh, H.: Efficient parallel and out of core algorithms for constructing large bi-directed de bruijn graphs. CoRR abs/1003.1940 (2010)
15. Mahmood, S.F., Rangwala, H.: Gpu-euler: Sequence assembly using gpgpu. In: Proceedings of the 2011 IEEE International Conference on High Performance Computing and Communications, HPCC 2011, pp. 153-160. IEEE Computer Society (2011)
16. National Center for Biotechnology Information, http://www.ncbi.nlm.nih. gov/