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instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder

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Baudry, Lyam | Guiglielmoni, Nadège | Marie-Nelly, Hervé | Cormier, Alexandre | Avia, Komlan | Marbouty, Martial | Mie, Yann Loe | Godfroy, Olivier | Sterck, Lieven | Cock, J. Mark | Zimmer, Christophe | Coelho, Susana | Koszul, Romain

Edité par CCSD ; BioMed Central -

International audience. Hi-C exploits contact frequencies between pairs of loci to bridge and order contigs during genome assembly, resulting in chromosome-level assemblies. Because few robust programs are available for this type of data, we developed instaGRAAL, a complete overhaul of the GRAAL program, which has adapted the latter to allow efficient assembly of large genomes. instaGRAAL features a number of improvements over GRAAL, including a modular correction approach that optionally integrates independent data. We validate the program using data for two brown algae, and human, to generate near-complete assemblies with minimal human intervention.

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