On Maximum Likelihood Reconstruction over Multiple Deletion Channels

Abstract

The problem of reconstructing a sequence when observed through multiple looks over deletion channels occurs in “de novo” DNA sequencing. The DNA could be sequenced multiple times, yielding several “looks” of it, but each time the sequencer could be noisy with (independent) deletion impairments. The main goal of this paper is to develop reconstruction algorithms for a sequence observed through the lens of a fixed number of deletion channels. We use the probabilistic model of the deletion channels to develop both symbol-wise and sequence maximum likelihood decoding criteria, and algorithms motivated by them. Numerical evaluations demonstrate improvement in terms of edit distance error, over earlier algorithms,