M. Abseher, N. Musliu, and S. Woltran, htd -A free, open-source framework for (customized) tree decompositions and beyond, Proc. of the 14th International Conference on Integration of AI and OR Techniques in Constraint Programming, vol.10335, pp.376-386, 2017.

M. A. Biscotti, E. Olmo, and J. S. Heslop-harrison, Repetitive DNA in eukaryotic genomes, Chromosome Res, vol.23, issue.3, pp.415-420, 2015.

P. Bongartz, Resolving repeat families with long reads, BMC Bioinformatics, vol.20, issue.232, pp.5-2019

A. Chateau and R. Giroudeau, A complexity and approximation framework for the maximization scaffolding problem, Theoretical Computer Science, vol.595, pp.92-106, 2015.
URL : https://hal.archives-ouvertes.fr/lirmm-01219622

D. S. Johnson, C. H. Papadimitriou, and M. Yannakakis, How easy is local search?, J. Comput. Syst. Sci, vol.37, issue.1, pp.79-100, 1988.

T. Kloks and . Treewidth, Computations and Approximations, vol.842, 1994.

M. Krentel, On finding and verifying locally optimal solutions, SIAM Journal on Computing, vol.19, issue.4, pp.742-749, 1990.

I. Mandric, J. Lindsay, I. I. M?ndoiu, and A. Zelikovsky, Scaffolding algorithms, Computational Methods for Next Generation Sequencing Data Analysis, pp.107-132, 2016.

A. A. Schäffer and M. Yannakakis, Simple local search problems that are hard to solve, SIAM J. Comput, vol.20, issue.1, pp.56-87, 1991.

D. Tabary, T. Davot, A. Chateau, R. Giroudeau, and M. Weller, New results about the linearization of scaffolds sharing repeated contigs, COCOA 2018, pp.94-107, 2018.
URL : https://hal.archives-ouvertes.fr/lirmm-01900389

H. Tang, Genome assembly, rearrangement, and repeats, Chemical Reviews, vol.107, issue.8, pp.3391-3406, 2007.

A. I. Tomescu, T. Gagie, A. Popa, R. Rizzi, A. Kuosmanen et al., Explaining a weighted DAG with few paths for solving genome-guided multiassembly, IEEE/ACM Trans. Comp. Biology Bioinform, vol.12, issue.6, pp.1345-1354, 2015.

A. Ummat and A. Bashir, Resolving complex tandem repeats with long reads, Bioinformatics, vol.30, issue.24, pp.3491-3498, 2014.

M. Weller, A. Chateau, and R. Giroudeau, Exact approaches for scaffolding, BMC Bioinformatics, vol.16, p.2, 2015.
URL : https://hal.archives-ouvertes.fr/lirmm-01219627

M. Weller, A. Chateau, and R. Giroudeau, On the linearization of scaffolds sharing repeated contigs, Combinatorial Optimization and Applications -11th International Conference, pp.509-517, 2017.
URL : https://hal.archives-ouvertes.fr/lirmm-01672893

M. Weller, A. Chateau, C. Dallard, and R. Giroudeau, Scaffolding problems revisited: Complexity, approximation and fixed parameter tractable algorithms, and some special cases, Algorithmica, vol.80, issue.6, pp.1771-1803, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01833303

M. Weller, A. Chateau, R. Giroudeau, and M. Poss, Scaffolding with repeated contigs using flow formulations, 2018.