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

par Baudry, Lyam;Guiglielmoni, Nadege ;Marie-Nelly, Hervé;Cormier, Alexandre;Marbouty, Martial;Avia, Komlan;Mie, Yann Loe;Godfroy, Olivier;Sterck, Lieven;Cock, Mark J.M.;Zimmer, Christophe;Coelho, Susana Margarida;Koszul, Romain
Référence Genome biology, 21, 1, page (148)
Publication Publié, 2020-06

Article révisé par les pairs

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Résumé :

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.