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

Naji Mounsef, Lina Karam, Zoé Lacroix, Christophe Legendre

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

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.

Original languageEnglish (US)
Title of host publicationGENSIPS'08 - 6th IEEE International Workshop on Genomic Signal Processing and Statistics
DOIs
StatePublished - Sep 17 2008
Event6th IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'08 - Phoenix, AZ, United States
Duration: Jun 8 2008Jun 10 2008

Publication series

NameGENSIPS'08 - 6th IEEE International Workshop on Genomic Signal Processing and Statistics

Other

Other6th IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'08
CountryUnited States
CityPhoenix, AZ
Period6/8/086/10/08

ASJC Scopus subject areas

  • Genetics
  • Signal Processing
  • Electrical and Electronic Engineering
  • Statistics, Probability and Uncertainty

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  • Cite this

    Mounsef, N., Karam, L., Lacroix, Z., & Legendre, C. (2008). A low-complexity probabilistic genome assembly based on hashing functions with SNP detection. In GENSIPS'08 - 6th IEEE International Workshop on Genomic Signal Processing and Statistics [4555676] (GENSIPS'08 - 6th IEEE International Workshop on Genomic Signal Processing and Statistics). https://doi.org/10.1109/GENSIPS.2008.4555676