On the Linearization of Scaffolds Sharing Repeated Contigs

Mathias Weller (1, 2) , Annie Chateau (1, 2) , Rodolphe Giroudeau (3)

1 IBC - Institut de Biologie Computationnelle
2 MAB - Méthodes et Algorithmes pour la Bioinformatique
3 MAORE - Methods, Algorithms for Operations REsearch

Scaffolding is the final step in assembling Next Generation Sequencing data, in which pre-assembled contiguous regions (“contigs”) are oriented and ordered using information that links them (for example, mapping of paired-end reads). As the genome of some species is highly repetitive, we allow placing some contigs multiple times, thereby generalizing established computational models for this problem. We study the subsequent problems induced by the translation of solutions of the model back to actual sequences, proposing models and analyzing the complexity of the resulting computational problems. We find both polynomial-time and $NP$ -hard special cases like planarity or bounded degree.

Domaines: Complexité [cs.CC]; Bio-Informatique, Biologie Systémique [q-bio.QM]

Mathias Weller, Annie Chateau, Rodolphe Giroudeau. On the Linearization of Scaffolds Sharing Repeated Contigs. COCOA: Conference on Combinatorial Optimization and Applications, Dec 2017, Shanghai, China. pp.509-517, ⟨10.1007/978-3-319-71147-8_38⟩. ⟨lirmm-01672893⟩