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instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder
Baudry, L.; Guiglielmoni, N.; Marie-Nelly, H.; Cormier, A.; Marbouty, M.; Avia, K.; Mie, Y.L.; Godfroy, O.; Sterck, L.; Cock, J.M.; Zimmer, C.; Coelho, S.M.; Koszul, R. (2020). instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder. Genome Biol. 21(1): 148. https://hdl.handle.net/10.1186/s13059-020-02041-z
In: Genome Biology. BioMed Central: London. ISSN 1465-6906; e-ISSN 1465-6914, more
Peer reviewed article  

Available in  Authors 

Keywords
    Desmarestia herbacea (Turner) J.V.Lamouroux, 1813 [WoRMS]; Ectocarpus Lyngbye, 1819 [WoRMS]
    Marine/Coastal
Author keywords
    Ectocarpus; Hi-C scaffolding; Hi-C; genome assembly; MCMC; GPU; Desmarestia herbacea

Authors  Top 
  • Baudry, L.
  • Guiglielmoni, N., more
  • Marie-Nelly, H.
  • Cormier, A.
  • Marbouty, M.
  • Avia, K.
  • Mie, Y.L.
  • Godfroy, O.
  • Sterck, L., more
  • Cock, J.M.
  • Zimmer, C.
  • Coelho, S.M.
  • Koszul, R.

Abstract
    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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