In this article we present MeDuSa (Multi-Draft based Scaffolder), an algorithm for genome scaffolding. MeDuSa exploits information obtained from a set of (draft or closed) genomes from related organisms to determine the correct order and orientation of the contigs. MeDuSa formalizes the scaffolding problem by means of a combinatorial optimization formulation on graphs and implements an efficient constant factor approximation algorithm to solve it. In contrast to currently used scaffolders, it does not require either prior knowledge on the microrganisms dataset under analysis (e.g. their phylogenetic relationships) or the availability of paired end read libraries. This makes usability and running time two additional important features of our method. Moreover, benchmarks and tests on real bacterial datasets showed that MeDuSa is highly accurate and, in most cases, outperforms traditional scaffolders. The possibility to use MeDuSa on eukaryotic datasets has also been evaluated, leading to interesting results.

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International audienceIn this paper, we study the problem of reconstructing special lattice sets from X-rays in a finite set of prescribed directions. We present the class of "Q-convex" sets which is a new class of subsets of Z2 having a certain kind of weak connectedness. The main result of this paper is a polynomial-time algorithm solving the reconstruction problem for the "Q-convex" sets. These sets are uniquely determined by certain finite sets of directions. As a result, this algorithm can be used for reconstructing convex subsets of Z2 from their X-rays in some suitable sets of four lattice directions or in any set of seven mutually non parallel lattice directions

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