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Genome assembly is a fundamental problem in Bioinformatics, requiring to reconstruct a source genome from an assembly graph built from a set of reads (short strings sequenced from the genome). A notion of genome assembly solution is that of an arc-covering walk of the graph. Since assembly graphs admit many solutions, the goal is to find what is definitely present in all solutions, or what is safe. Most practical assemblers are based on heuristics having at their core unitigs, namely paths whose internal nodes have unit in-degree and out-degree, and which are clearly safe. The long-standing open problem of finding all the safe parts of the solutions was recently solved by a major theoretical result [RECOMB16]. This safe and complete genome assembly algorithm was followed by other works improving the time bounds, as well as extending the results for different notions of assembly solution. But it remained open whether one can be complete also for models of genome assembly of practical applicability. In this paper we present a universal framework for obtaining safe and complete algorithms which unify the previous results, while also allowing for easy generalisations to assembly problems including many practical aspects. This is based on a novel graph structure, called the hydrostructure of a walk, which highlights the reachability properties of the graph from the perspective of the walk. The hydrostructure allows for simple characterisations of the existing safe walks, and of their new practic
We develop a framework for the rigorous analysis of focused stochastic local search algorithms. These are algorithms that search a state space by repeatedly selecting some constraint that is violated in the current state and moving to a random nearby
Given two independent sets $I, J$ of a graph $G$, and imagine that a token (coin) is placed at each vertex of $I$. The Sliding Token problem asks if one could transform $I$ to $J$ via a sequence of elementary steps, where each step requires sliding a
Current models for the folding of the human genome see a hierarchy stretching down from chromosome territories, through A/B compartments and TADs (topologically-associating domains), to contact domains stabilized by cohesin and CTCF. However, molecul
An edge-coloring of a graph $G$ with colors $1,2,ldots,t$ is an interval $t$-coloring if all colors are used, and the colors of edges incident to each vertex of $G$ are distinct and form an interval of integers. A graph $G$ is interval colorable if i
In this short note, we show two NP-completeness results regarding the emph{simultaneous representation problem}, introduced by Lubiw and Jampani. The simultaneous representation problem for a given class of intersection graphs asks if some $k$ graphs