Comparative Genomics of Non-Model Invertebrates

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Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms

Nadège Guiglielmoni, Antoine Houtain, Alessandro Derzelle, Karine Van Doninck, Jean-François Flot
YEAR: 2021
PUBLISHER/PLACE: BioMed Central
JOURNAL: BMC Bioinformatics
VOLUME/ISSUE: 22
PAGES: 303
URL/DOI: https://doi.org/10.1186/s12859-021-04118-3

GraphUnzip: unzipping assembly graphs with long reads and Hi-C

Roland Faure, ProfileNadège Guiglielmoni, ProfileJean-François Flot
YEAR: 2021
JOURNAL: bioRxiv
URL/DOI: https://doi.org/10.1101/2021.01.29.428779

Homologous chromosomes in asexual rotifer Adineta vaga suggest automixis

Paul Simion, Jitendra Narayan, Antoine Houtain, Alessandro Derzelle, Lyam Baudry, Emilien Nicolas, Marie Cariou, Nadège Guiglielmoni, Djampa KL Kozlowski, Florence Rodriguez Gaudray, Matthieu Terwagne, Julie Virgo, Benjamin Noel, Patrick Wincker, Etienne GJ Danchin, Martial Marbouty, Bernard Hallet, Romain Koszul, Antoine Limasset, Jean-François Flot, Karine Van Doninck
YEAR: 2020
JOURNAL: bioRxiv
URL/DOI: https://doi.org/10.1101/2020.06.16.155473

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

Lyam Baudry, Nadège Guiglielmoni, Hervé Marie-Nelly, Alexandre Cormier, Martial Marbouty, Komlan Avia, Yann Loe Mie, Olivier Godfroy, Lieven Sterck, J. Mark Cock, Christophe Zimmer, Susana M. Coelho
YEAR: 2020
PUBLISHER/PLACE: BioMed Central
JOURNAL: Genome Biology
VOLUME/ISSUE: 21/1
PAGES: 148
URL/DOI: https://doi.org/10.1186/s13059-020-02041-z

Computer vision for pattern detection in chromosome contact maps

Cyril Matthey-Doret, Lyam Baudry, Axel Breuer, Rémi Montagne, Nadège Guiglielmoni, Vittore Scolari, Etienne Jean, Arnaud Campeas, Philippe Henri Chanut, Edgar Oriol, Adrien Méot, Laurent Politis, Antoine Vigouroux, Pierrick Moreau, Romain Koszul, Axel Cournac
YEAR: 2020
PUBLISHER/PLACE: Nature Publishing Group
JOURNAL: Nature Communications
VOLUME/ISSUE: 11/1
PAGES: 5795
URL/DOI: https://doi.org/10.1038/s41467-020-19562-7