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

  • Baudry, Lyam1, 2
  • Guiglielmoni, Nadège1, 3
  • Marie-Nelly, Hervé1, 2
  • Cormier, Alexandre4
  • Marbouty, Martial1
  • Avia, Komlan4, 5
  • Mie, Yann Loe6
  • Godfroy, Olivier4
  • Sterck, Lieven7, 8
  • Cock, J. Mark4
  • Zimmer, Christophe9
  • Coelho, Susana M.4
  • Koszul, Romain1
  • 1 Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, C3BI USR 3756, Paris, F-75015, France , Paris (France)
  • 2 Sorbonne Université, Collège Doctoral, Paris, F-75005, France , Paris (France)
  • 3 Université Libre de Bruxelles, Brussels, 1050, Belgium , Brussels (Belgium)
  • 4 Sorbonne Université, Laboratory of Integrative Biology of Marine Models, Algal Genetics, UMR 8227, Roscoff, France , Roscoff (France)
  • 5 Present Address: Université de Strasbourg, INRA, SVQV UMR-A 1131, Colmar, France , Colmar (France)
  • 6 Institut Pasteur, Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), USR3756, CNRS, Paris, France , Paris (France)
  • 7 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052 Ghent, Belgium , Ghent (Belgium)
  • 8 VIB Center for Plant Systems Biology, Technologiepark 927, Ghent, B-9052, Belgium , Ghent (Belgium)
  • 9 Institut Pasteur, Imaging and Modeling Unit, CNRS, UMR 3691, C3BI USR 3756, Paris, F-75015, France , Paris (France)
Published Article
Publication Date
Jun 18, 2020
DOI: 10.1186/s13059-020-02041-z
Springer Nature


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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