Reference-based DNA shotgun sequencing: Information theoretic limits

The reference-based DNA shotgun assembly problem is studied from an information-theoretic point of view. The entire sequence has to be assembled based on a reference sequence which is a noisy version of the desired one, and a set of short reads sampled from the desired sequence. Two necessary conditions on the underlying parameters for reconstruction are obtained. A reference-based assembly algorithm is proposed, and it is shown that under these conditions the algorithm can reconstruct the sequence with high probability.