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IEEE 21st Annual International Symposium on Field-Programmable Custom Computing Machines (FCCM 2013) (2013)
Seattle, WA
April 28, 2013 to April 30, 2013
ISBN: 978-1-4673-6005-0
pp: 173-176
B. Sharat Chandra Varma , Dept. of Comput. Sci. & Eng., Indian Inst. of Technol. Delhi, New Delhi, India
Kolin Paul , Dept. of Comput. Sci. & Eng., Indian Inst. of Technol. Delhi, New Delhi, India
M. Balakrishnan , Dept. of Comput. Sci. & Eng., Indian Inst. of Technol. Delhi, New Delhi, India
Dominique Lavenier , IRISA, INRIA, Rennes, France
ABSTRACT
Next generation sequencing technologies produce large amounts of data at very low cost. They produce short reads of DNA fragments. These fragments have many overlaps, lots of repeats and may also include sequencing errors. The assembly process involves merging these sequences to form the original sequences. In recent years many software programs have been developed for this purpose. All of them take significant amount of time to execute. Velvet is a commonly used de novo assembly program. We propose a method to reduce the overall time for assembly by using pre-processing of the short read data on FPGAs and processing its output using Velvet. We show significant speed-ups with slight or no compromise on the quality of the assembled output.
INDEX TERMS
Field programmable gate arrays, Assembly, Bioinformatics, Software, Genomics, Acceleration, Redundancy,Bioinformatics, FPGA, Acceleration, Next Generation Sequencing Assembly
CITATION
B. Sharat Chandra Varma, Kolin Paul, M. Balakrishnan, Dominique Lavenier, "FAssem: FPGA Based Acceleration of De Novo Genome Assembly", IEEE 21st Annual International Symposium on Field-Programmable Custom Computing Machines (FCCM 2013), vol. 00, no. , pp. 173-176, 2013, doi:10.1109/FCCM.2013.25
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