Optimal Assembly for High Throughput Shotgun Sequencing

We present a framework for the design of optimal assembly algorithms for shotgun sequencing under the criterion of complete reconstruction. We derive a lower bound on the read length and the coverage depth required for reconstruction in terms of the repeat statistics of the genome. Building on earli...

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Bibliographic Details
Published inarXiv.org
Main Authors Bresler, Guy, Bresler, Ma'ayan, Tse, David
Format Paper
LanguageEnglish
Published Ithaca Cornell University Library, arXiv.org 18.02.2013
Subjects
Algorithms
Assembly
Deoxyribonucleic acid
DNA
Genomes
Lower bounds
Reconstruction
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Summary:We present a framework for the design of optimal assembly algorithms for shotgun sequencing under the criterion of complete reconstruction. We derive a lower bound on the read length and the coverage depth required for reconstruction in terms of the repeat statistics of the genome. Building on earlier works, we design a de Brujin graph based assembly algorithm which can achieve very close to the lower bound for repeat statistics of a wide range of sequenced genomes, including the GAGE datasets. The results are based on a set of necessary and sufficient conditions on the DNA sequence and the reads for reconstruction. The conditions can be viewed as the shotgun sequencing analogue of Ukkonen-Pevzner's necessary and sufficient conditions for Sequencing by Hybridization.
ISSN:2331-8422