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.
CITATION STYLE
Bresler, G., Bresler, M., & Tse, D. (2013). Optimal assembly for high throughput shotgun sequencing. BMC Bioinformatics, 14 Suppl 5. https://doi.org/10.1186/1471-2105-14-s5-s18
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