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 - 2008
Event6th IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'08 - Phoenix, AZ, United States
Duration: Jun 8 2008Jun 10 2008

Other

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

Fingerprint

Hashing
Low Complexity
Single Nucleotide Polymorphism
Genome
Genes
Aptitude
Efficiency
Genomics
Completeness
Data storage equipment

ASJC Scopus subject areas

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

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] https://doi.org/10.1109/GENSIPS.2008.4555676

A low-complexity probabilistic genome assembly based on hashing functions with SNP detection. / Mounsef, Naji; Karam, Lina; Lacroix, Zoé; Legendre, Christophe.

GENSIPS'08 - 6th IEEE International Workshop on Genomic Signal Processing and Statistics. 2008. 4555676.

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

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, 6th IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'08, Phoenix, AZ, United States, 6/8/08. https://doi.org/10.1109/GENSIPS.2008.4555676
Mounsef N, Karam L, Lacroix Z, Legendre C. 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. 2008. 4555676 https://doi.org/10.1109/GENSIPS.2008.4555676
Mounsef, Naji ; Karam, Lina ; Lacroix, Zoé ; Legendre, Christophe. / A low-complexity probabilistic genome assembly based on hashing functions with SNP detection. GENSIPS'08 - 6th IEEE International Workshop on Genomic Signal Processing and Statistics. 2008.
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