دورية أكاديمية
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
| العنوان: | Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species |
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| المؤلفون: | Bradnam, Keith, Fass, Joseph, Alexandrov, Anton, Baranay, Paul, Bechner, Michael, Birol, Inanç, Boisvert, Sébastien, Chapman, Jarrod, Chapuis, Guillaume, Chikhi, Rayan, Chitsaz, Hamidreza, Chou, Wen-Chi, Corbeil, Jacques, del Fabbro, Cristian, Docking, T, Roderick, Durbin, Richard, Earl, Dent, Emrich, Scott, Fedotov, Pavel, Fonseca, Nuno, Ganapathy, Ganeshkumar, Gibbs, Richard, Gnerre, Sante, Godzaridis, Élénie, Goldstein, Steve, Haimel, Matthias, Hall, Giles, Haussler, David, Hiatt, Joseph, Ho, Isaac, Howard, Jason, Hunt, Martin, Jackman, Shaun, Jaffe, David, Jarvis, Erich, Jiang, Huaiyang, Kazakov, Sergey, Kersey, Paul, Kitzman, Jacob, Knight, James, Koren, Sergey, Lam, Tak-Wah, Lavenier, Dominique, Laviolette, François, Li, Yingrui, Li, Zhenyu, Liu, Binghang, Liu, Yue, Luo, Ruibang, Maccallum, Iain, Macmanes, Matthew, Maillet, Nicolas, Melnikov, Sergey, Naquin, Delphine, Ning, Zemin, Otto, Thomas, Paten, Benedict, Paulo, Octávio, Phillippy, Adam, Pina-Martins, Francisco, Place, Michael, Przybylski, Dariusz, Qin, Xiang, Qu, Carson, Ribeiro, Filipe, Richards, Stephen, Rokhsar, Daniel, Ruby, J, Graham, Scalabrin, Simone, Schatz, Michael, Schwartz, David, Sergushichev, Alexey, Sharpe, Ted, Shaw, Timothy, Shendure, Jay, Shi, Yujian, Simpson, Jared, Song, Henry, Tsarev, Fedor, Vezzi, Francesco, Vicedomini, Riccardo, Vieira, Bruno, Wang, Jun, Worley, Kim, Yin, Shuangye, Yiu, Siu-Ming, Yuan, Jianying, Zhang, Guojie, Zhang, Hao, Zhou, Shiguo, Korf, Ian |
| المساهمون: | Genome Center UC Davis, University of California Davis (UC Davis), University of California (UC)-University of California (UC), National Research University of Information Technologies, Mechanics and Optics St. Petersburg (ITMO), Computational Biology and Bioinformatics New Haven, Yale University New Haven, Laboratory for Molecular and Computational Genomics Madison, University of Wisconsin-Madison, Genome Sciences Centre Vancouver (GSC), British Columbia Cancer Agency, Infectious Diseases Research Center Québec, Université Laval Québec (ULaval), Faculté de médecine de l'Université Laval Québec (ULaval), DOE Joint Genome Institute Walnut Creek, Biological systems and models, bioinformatics and sequences (SYMBIOSE), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), Dependability Interoperability and perfOrmance aNalYsiS Of networkS (DIONYSOS), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-RÉSEAUX, TÉLÉCOMMUNICATION ET SERVICES (IRISA-D2), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Department of computer science Detroit, Wayne State University Detroit, Institute of Bioinformatics Athens, University of Georgia USA, Institute of Aging Research Boston, Hebrew SeniorLife Boston, Department of Molecular Medicine Québec, Institute of Applied Genomics Udine (IGA), Institute of Applied Genomics, The Wellcome Trust Sanger Institute Cambridge, Howard Hughes Medical Institute Santa Cruz (HHMI), Howard Hughes Medical Institute (HHMI)-University of California Santa Cruz (UC Santa Cruz), Department of Computer Science and Engineering South Bend, University of Notre Dame Indiana (UND), European Bioinformatics Institute Hinxton (EMBL-EBI), EMBL Heidelberg, CRACS & Inesc TEC Porto, Universidade do Porto = University of Porto, Medical Center Durham, Duke University Durham, Human Genome Sequencing Center Houston (HGSC), Baylor College of Medicine (BCM), Baylor University-Baylor University, Broad Institute Cambridge, Harvard University-Massachusetts Institute of Technology (MIT), Faculty of Medicine, Department of Genome Sciences Seattle (GS), University of Washington Seattle, 454 Life Sciences Branford, 454 Life Sciences, National Biodefense Analysis and Countermeasures Center Frederick, U.S. Social Security Administration, Center for Bioinformatics and Computational Biology Maryland (CBCB), University of Maryland College Park, University of Maryland System-University of Maryland System, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory Hong Kong, The University of Hong Kong (HKU), Invariant Preserving SOlvers (IPSO), Institut de Recherche Mathématique de Rennes (IRMAR), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Department of Computer Science and Software Engineering Québec, Beijing Genomics Institute Shenzhen (BGI), Berkeley California Institute for Quantitative Biosciences Berkeley, University of California (UC), Computational Biology & Population Genomics Group Lisboa, Centre for Environmental Biology, New York Genome Center New York, New York Genome Center, Department of Molecular and Cell Biology, Department of Biochemistry and Biophysics, Howard Hughes Medical Institute (HHMI), Simons Center for Quantitative Biology Cold Spring Harbor, Cold Spring Harbor Laboratory, Department of Epidemiology and Biostatistics Athens, University of Georgia USA -College of Public Health, Science for Life Laboratory Solna, KTH Royal Institute of Technology Stockholm (KTH ), Department of Mathematics and Computer Science Udine, Università degli Studi di Udine - University of Udine Italie |
| المصدر: | EISSN: 2047-217X ; GigaScience ; https://inria.hal.science/hal-00868822Test ; GigaScience, 2013, 2 (1), pp.10. ⟨10.1186/2047-217X-2-10⟩ ; http://www.gigasciencejournal.com/content/2/1/10Test |
| بيانات النشر: | HAL CCSD Oxford Univ Press |
| سنة النشر: | 2013 |
| المجموعة: | Archive Ouverte de l'Université Rennes (HAL) |
| مصطلحات موضوعية: | [INFO.INFO-AR]Computer Science [cs]/Hardware Architecture [cs.AR] |
| الوصف: | International audience ; Background The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another. |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | English |
| العلاقة: | hal-00868822; https://inria.hal.science/hal-00868822Test; https://inria.hal.science/hal-00868822/documentTest; https://inria.hal.science/hal-00868822/file/2047-217X-2-10.pdfTest |
| DOI: | 10.1186/2047-217X-2-10 |
| الإتاحة: | https://doi.org/10.1186/2047-217X-2-10Test https://inria.hal.science/hal-00868822Test https://inria.hal.science/hal-00868822/documentTest https://inria.hal.science/hal-00868822/file/2047-217X-2-10.pdfTest |
| حقوق: | info:eu-repo/semantics/OpenAccess |
| رقم الانضمام: | edsbas.31A76116 |
| قاعدة البيانات: | BASE |
| DOI: | 10.1186/2047-217X-2-10 |
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