Optimal Assembly for High Throughput Shotgun Sequencing

• Published in: arXiv.org
• Main Authors: Bresler, Guy, Bresler, Ma'ayan, Tse, David
• Format: Paper
• Language: English
• Published: Ithaca Cornell University Library, arXiv.org 18.02.2013
• Subjects: Algorithms; Assembly; Deoxyribonucleic acid; DNA; Genomes; Lower bounds; Reconstruction

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...