دورية أكاديمية
instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder
| العنوان: | instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder |
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| المؤلفون: | Baudry, Lyam, Guiglielmoni, Nadège, Marie-Nelly, Hervé, Cormier, Alexandre, Avia, Komlan, Marbouty, Martial, Mie, Yann Loe, Godfroy, Olivier, Sterck, Lieven, Cock, J. Mark, Zimmer, Christophe, Coelho, Susana, Koszul, Romain |
| المساهمون: | Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur Paris (IP)-Centre National de la Recherche Scientifique (CNRS), Département de Biologie Computationnelle - Department of Computational Biology, Collège Doctoral, Sorbonne Université (SU), Université libre de Bruxelles (ULB), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff = Roscoff Marine Station (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Santé de la vigne et qualité du vin (SVQV), Université de Strasbourg (UNISTRA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biologie et Amélioration des Plantes (BAP), Universiteit Gent = Ghent University (UGENT), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie Ghent, Belgique (VIB), Imagerie et Modélisation - Imaging and Modeling, This research was supported by funding to R.K. and S.M.C. from the European Research Council under the Horizon 2020 Program (ERC grant agreements 260822 and 638240, respectively). This project has also received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No 764840., European Project: 260822,EC:FP7:ERC,ERC-2010-StG_20091118,DICIG(2011), European Project: 638240,H2020,ERC-2014-STG,SEXSEA(2015), European Project: 764840,H2020-EU.1.3. - EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions / H2020-EU.1.3.1. - Fostering new skills by means of excellent initial training of researchers,10.3030/764840,IGNITE(2018) |
| المصدر: | ISSN: 1465-6906. |
| بيانات النشر: | HAL CCSD BioMed Central |
| سنة النشر: | 2020 |
| المجموعة: | Institut Pasteur: HAL |
| مصطلحات موضوعية: | [SDV]Life Sciences [q-bio], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] |
| الوصف: | International audience ; 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. |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | English |
| العلاقة: | info:eu-repo/semantics/altIdentifier/pmid/32552806; info:eu-repo/grantAgreement/EC/FP7/260822/EU/Dynamic Interplay between Eukaryotic Chromosomes: Impact on Genome Stability/DICIG; info:eu-repo/grantAgreement//638240/EU/Origin and evolution of the sexes and reproductive systems: novel insights from a distant eukaryotic lineage/SEXSEA; info:eu-repo/grantAgreement//764840/EU/Comparative genomics of non-model invertebrates/IGNITE; pasteur-02873422; https://pasteur.hal.science/pasteur-02873422Test; https://pasteur.hal.science/pasteur-02873422/documentTest; https://pasteur.hal.science/pasteur-02873422/file/Baudry_GB_2020.pdfTest; PUBMED: 32552806; PUBMEDCENTRAL: PMC7386250; WOS: 000542999600001 |
| DOI: | 10.1186/s13059-020-02041-z |
| الإتاحة: | https://doi.org/10.1186/s13059-020-02041-zTest https://pasteur.hal.science/pasteur-02873422Test https://pasteur.hal.science/pasteur-02873422/documentTest https://pasteur.hal.science/pasteur-02873422/file/Baudry_GB_2020.pdfTest |
| حقوق: | http://creativecommons.org/licenses/byTest/ ; info:eu-repo/semantics/OpenAccess |
| رقم الانضمام: | edsbas.E200ECDE |
| قاعدة البيانات: | BASE |
| DOI: | 10.1186/s13059-020-02041-z |
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