Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Keith Bradnam 1, * Joseph Fass 1 Anton Alexandrov 2 Paul Baranay 3 Michael Bechner 4 Inanç Birol 5 Sébastien Boisvert 6, 7 Jarrod Chapman 8 Guillaume Chapuis 9, 10 Rayan Chikhi 1 Hamidreza Chitsaz 11 Wen-Chi Chou 12, 13 Jacques Corbeil 6, 14 Cristian Del Fabbro 15 T Docking 5 Richard Durbin 16 Dent Earl 17 Scott Emrich 18 Pavel Fedotov 2 Nuno Fonseca 19, 20 Ganeshkumar Ganapathy 21 Richard Gibbs 22 Sante Gnerre 23 Élénie Godzaridis 24 Steve Goldstein 4 Matthias Haimel 19 Giles Hall 23 David Haussler 17 Joseph Hiatt 25 Isaac Ho 8 Jason Howard 21 Martin Hunt 16 Shaun Jackman 5 David Jaffe 23 Erich Jarvis 21 Huaiyang Jiang 22 Sergey Kazakov 2 Paul Kersey 19 Jacob Kitzman 25 James Knight 26 Sergey Koren 27, 28 Tak-Wah Lam 29 Dominique Lavenier 30, 9, 10 François Laviolette 31 Yingrui Li 32, 29 Zhenyu Li 32 Binghang Liu 32 Yue Liu 22 Ruibang Luo 32, 29 Iain Maccallum 23 Matthew Macmanes 33 Nicolas Maillet 30, 9 Sergey Melnikov 2 Delphine Naquin 30, 9 Zemin Ning 16 Thomas Otto 16 Benedict Paten 17 Octávio Paulo 34 Adam Phillippy 27, 28 Francisco Pina-Martins 34 Michael Place 4 Dariusz Przybylski 23 Xiang Qin 22 Carson Qu 22 Filipe Ribeiro 35 Stephen Richards 22 Daniel Rokhsar 8, 36 J Ruby 37, 38 Simone Scalabrin 15 Michael Schatz 39 David Schwartz 4 Alexey Sergushichev 2 Ted Sharpe 23 Timothy Shaw 12, 40 Jay Shendure 25 Yujian Shi 32 Jared Simpson 16 Henry Song 22 Fedor Tsarev 2 Francesco Vezzi 41 Riccardo Vicedomini 15, 42 Bruno Vieira 34 Jun Wang 32 Kim Worley 22 Shuangye Yin 23 Siu-Ming Yiu 29 Jianying Yuan 32 Guojie Zhang 32 Hao Zhang 32 Shiguo Zhou 4 Ian Korf 1, *
* Auteur correspondant
9 SYMBIOSE - Biological systems and models, bioinformatics and sequences
IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires, Inria Rennes – Bretagne Atlantique
10 DIONYSOS - Dependability Interoperability and perfOrmance aNalYsiS Of networkS
Inria Rennes – Bretagne Atlantique , IRISA-D2 - RÉSEAUX, TÉLÉCOMMUNICATION ET SERVICES
30 IPSO - Invariant Preserving SOlvers
IRMAR - Institut de Recherche Mathématique de Rennes, Inria Rennes – Bretagne Atlantique
Abstract : 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.
Type de document :
Article dans une revue
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https://hal.inria.fr/hal-00868822
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Soumis le : mercredi 2 octobre 2013 - 06:11:30
Dernière modification le : vendredi 22 juin 2018 - 01:13:41
Document(s) archivé(s) le : vendredi 7 avril 2017 - 05:05:57

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Citation

Keith Bradnam, Joseph Fass, Anton Alexandrov, Paul Baranay, Michael Bechner, et al.. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience, BioMed Central, 2013, 2 (1), pp.10. 〈http://www.gigasciencejournal.com/content/2/1/10〉. 〈10.1186/2047-217X-2-10 〉. 〈hal-00868822〉

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