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

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

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.