Hierarchical Overlap Graph (1802.04632v2)

Abstract: Given a set of finite words, the Overlap Graph (OG) is a complete weighted digraph where each word is a node and where the weight of an arc equals the length of the longest overlap of one word onto the other (Overlap is an asymmetric notion). The OG serves to assemble DNA fragments or to compute shortest superstrings which are a compressed representation of the input. The OG requires a space is quadratic in the number of words, which limits its scalability. The Hierarchical Overlap Graph (HOG) is an alternative graph that also encodes all maximal overlaps, but uses a space that is linear in the sum of the lengths of the input words. We propose the first algorithm to build the HOG in linear space for words of equal length.