Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
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- 作者：Keith R Bradnam (1)
Joseph N Fass (1)
Anton Alexandrov (36)
Paul Baranay (2)
Michael Bechner (39)
Inan? Birol (33)
Sébastien Boisvert (10) (11)
Jarrod A Chapman (20)
Guillaume Chapuis (7) (9)
Rayan Chikhi (7) (9)
Hamidreza Chitsaz (6)
Wen-Chi Chou (14) (16)
Jacques Corbeil (10) (13)
Cristian Del Fabbro (17)
T Roderick Docking (33)
Richard Durbin (34)
Dent Earl (40)
Scott Emrich (3)
Pavel Fedotov (36)
Nuno A Fonseca (30) (35)
Ganeshkumar Ganapathy (38)
Richard A Gibbs (32)
Sante Gnerre (22)
élénie Godzaridis (11)
Steve Goldstein (39)
Matthias Haimel (30)
Giles Hall (22)
David Haussler (40)
Joseph B Hiatt (41)
Isaac Y Ho (20)
Jason Howard (38)
Martin Hunt (34)
Shaun D Jackman (33)
David B Jaffe (22)
Erich D Jarvis (38)
Huaiyang Jiang (32)
Sergey Kazakov (36)
Paul J Kersey (30)
Jacob O Kitzman (41)
James R Knight (37)
Sergey Koren (24) (25)
Tak-Wah Lam (29)
Dominique Lavenier (7) (8) (9)
Fran?ois Laviolette (12)
Yingrui Li (28) (29)
Zhenyu Li (28)
Binghang Liu (28)
Yue Liu (32)
Ruibang Luo (28) (29)
Iain MacCallum (22)
Matthew D MacManes (5)
Nicolas Maillet (8) (9)
Sergey Melnikov (36)
Delphine Naquin (8) (9)
Zemin Ning (34)
Thomas D Otto (34)
Benedict Paten (40)
Octávio S Paulo (31)
Adam M Phillippy (24) (25)
Francisco Pina-Martins (31)
Michael Place (39)
Dariusz Przybylski (22)
Xiang Qin (32)
Carson Qu (32)
Filipe J Ribeiro (23)
Stephen Richards (32)
Daniel S Rokhsar (20) (21)
J Graham Ruby (26) (27)
Simone Scalabrin (17)
Michael C Schatz (4)
David C Schwartz (39)
Alexey Sergushichev (36)
Ted Sharpe (22)
Timothy I Shaw (14) (15)
Jay Shendure (41)
Yujian Shi (28)
Jared T Simpson (34)
Henry Song (32)
Fedor Tsarev (36)
Francesco Vezzi (19)
Riccardo Vicedomini (17) (18)
Bruno M Vieira (31)
Jun Wang (28)
Kim C Worley (32)
Shuangye Yin (22)
Siu-Ming Yiu (29)
Jianying Yuan (28)
Guojie Zhang (28)
Hao Zhang (28)
Shiguo Zhou (39)
Ian F Korf (1) - 关键词：Genome assembly ; N50 ; Scaffolds ; Assessment ; Heterozygosity ; COMPASS
- 刊名：GigaScience
- 出版年：2013
- 出版时间：December 2013
- 年：2013
- 卷：2
- 期：1
- 全文大小：1,442 KB
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Joseph N Fass (1)
Anton Alexandrov (36)
Paul Baranay (2)
Michael Bechner (39)
Inan? Birol (33)
Sébastien Boisvert (10) (11)
Jarrod A Chapman (20)
Guillaume Chapuis (7) (9)
Rayan Chikhi (7) (9)
Hamidreza Chitsaz (6)
Wen-Chi Chou (14) (16)
Jacques Corbeil (10) (13)
Cristian Del Fabbro (17)
T Roderick Docking (33)
Richard Durbin (34)
Dent Earl (40)
Scott Emrich (3)
Pavel Fedotov (36)
Nuno A Fonseca (30) (35)
Ganeshkumar Ganapathy (38)
Richard A Gibbs (32)
Sante Gnerre (22)
élénie Godzaridis (11)
Steve Goldstein (39)
Matthias Haimel (30)
Giles Hall (22)
David Haussler (40)
Joseph B Hiatt (41)
Isaac Y Ho (20)
Jason Howard (38)
Martin Hunt (34)
Shaun D Jackman (33)
David B Jaffe (22)
Erich D Jarvis (38)
Huaiyang Jiang (32)
Sergey Kazakov (36)
Paul J Kersey (30)
Jacob O Kitzman (41)
James R Knight (37)
Sergey Koren (24) (25)
Tak-Wah Lam (29)
Dominique Lavenier (7) (8) (9)
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1. Genome Center, UC, Davis, CA, 95616, USA
36. National Research University of Information Technology, Mechanics and Optics (University ITMO), St. Petersburg, 197101, Russia
2. Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06511, USA
39. Laboratory for Molecular and Computational Genomics, Departments of Chemistry and Genetics, UW-Biotechnology Center, 425 Henry Mall, Madison, WI, 53706, USA
33. Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, V5Z 4E6, Canada
10. Infectious Diseases Research Center, Université Laval, Québec, QC, G1V 4G2, Canada
11. Faculty of Medicine, Université Laval, Québec, QC, G1V 4G2, Canada
20. DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
7. Computer Science department, ENS Cachan/IRISA, 35042, Rennes, France
9. CNRS/Symbiose, IRISA, 35042, Rennes, France
6. Department of Computer Science, Wayne State University, Detroit, MI, 48202, USA
14. Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
16. Institute of Aging Research, Hebrew SeniorLife, Boston, MA, 02131, USA
13. Department of Molecular Medicine, Faculty of Medicine, Université Laval, Québec, QC, G1V 4G2, Canada
17. IGA, Institute of Applied Genomics, 33100, Udine, Italy
34. The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
40. Howard Hughes Medical Institute, Center for Biomolecular Science & Engineering, University of California, Santa Cruz, CA, 95064, USA
3. Department of Computer Science and Engineering, University of Notre Dame, South Bend, IN, 46556, USA
30. EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
35. CRACS - INESC TEC, 4200-465, Porto, Portugal
38. Duke University Medical Center, Durham, NC, 27710, USA
32. Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
22. Broad Institute, Cambridge, MA, 02142, USA
41. Department of Genome Sciences, School of Medicine, University of Washington, Seattle, WA, 98195, USA
37. 454 Life Sciences, 15 Commercial Street, Branford, CT, 06405, USA
24. National Biodefense Analysis and Countermeasures Center, Frederick, MD, 21702, USA
25. Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA
29. HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Pok Fu Lam Rd, Hong Kong, Hong Kong
8. INRIA, Rennes Bretagne Atlantique, 35042, Rennes, France
12. Department of Computer Science and Software Engineering, Faculty of Science and Engineering, Université Laval, Québec, QC, G1V 4G2, Canada
28. BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
5. Berkeley California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
31. Computational Biology & Population Genomics Group, Centre for Environmental Biology, Department of Animal Biology, Faculty of Sciences of the University of Lisbon, Campo Grande, P-1749-016, Lisbon, Portugal
23. New York Genome Center, New York, NY, 10022, USA
21. Department of Molecular and Cell Biology, UC Berkeley, Berkeley, CA, 94720, USA
26. Department of Biochemistry and Biophysics, University of California, San Francisco, CA, 94143, USA
27. Howard Hughes Medical Institute, Bethesda, MD, 20814, USA
4. Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
15. Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, GA, 30602, USA
19. Science for Life Laboratory, KTH Royal Institute of Technology, 17121, Solna, Sweden
18. Department of Mathematics and Computer Science, University of Udine, 33100, Udine, Italy - ISSN：2047-217X
文摘
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.