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arXiv · 1301.0068

Optimal Assembly for High Throughput Shotgun Sequencing

Guy Bresler·Ma'ayan Bresler·David Tse
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Abstract

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.

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Guy Bresler, Ma'ayan Bresler, David Tse. 2013-02-18. Optimal Assembly for High Throughput Shotgun Sequencing. https://arxiv.org/abs/1301.0068

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