Paper at CPM 2021 conference
The hierarchical overlap graph (HOG for short) is an overlap encoding graph that efficiently represents overlaps from a given set $P$ of $n$ strings. A previously known algorithm constructs the HOG in $O(|| P || + n^2)$ time and $O(|| P || +n times …
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 …
The Maximum Asymmetric Travelling Salesman Problem (Max-ATSP), which asks for a Hamiltonian path of maximum weight covering a digraph, and the Maximum Compression(Max-Comp), which, for a finite language $P ≔s1,…,sp$, asks for w, a superstring of P …
Background. Next Generation Sequencing (NGS) has dramatically enhanced our ability to sequence genomes, but not to assemble them. In practice, many published genome sequences remain in the state of a large set of contigs. Each contig describes the …