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A low-complexity probabilistic genome assembly based on hashing functions with SNP detection

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4 Author(s)
Mounsef, N. ; Dept. of Electr. Eng., Arizona State Univ., Tempe, AZ ; Karam, L. ; Lacroix, Z. ; Legendre, C.

This paper presents an efficient low-complexity genome assembly algorithm with the ability to detect bit errors (SNPs). A hashing function is used to reduce the complexity of the assembly process. The algorithm is tested against genomic sequences of different lengths. Its performance in terms of completeness, accuracy, and efficiency (time and space) is evaluated against Phrap, a well-known sequence assembly tool. It is shown that the proposed assembly algorithm outperforms Phrap in terms of accuracy, time, and memory.

Published in:

Genomic Signal Processing and Statistics, 2008. GENSiPS 2008. IEEE International Workshop on

Date of Conference:

8-10 June 2008