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 Roderick 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 Graham 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)

1 Genome Center [UC Davis]
2 ITMO - National Research University of Information Technologies, Mechanics and Optics [St. Petersburg]
3 Computational Biology and Bioinformatics [New Haven]
4 Laboratory for Molecular and Computational Genomics [Madison]
5 GSC - Genome Sciences Centre [Vancouver]
6 Infectious Diseases Research Center [Québec]
7 ULaval - Faculté de médecine de l'Université Laval [Québec]
8 DOE Joint Genome Institute [Walnut Creek]
9 SYMBIOSE - Biological systems and models, bioinformatics and sequences
10 DIONYSOS - Dependability Interoperability and perfOrmance aNalYsiS Of networkS
11 Department of computer science [Detroit]
12 Institute of Bioinformatics [Athens]
13 Institute of Aging Research [Boston]
14 Department of Molecular Medicine [Québec]
15 IGA - Institute of Applied Genomics [Udine]
16 The Wellcome Trust Sanger Institute [Cambridge]
17 HHMI - Howard Hughes Medical Institute [Santa Cruz]
18 Department of Computer Science and Engineering [South Bend]
19 EMBL-EBI - European Bioinformatics Institute [Hinxton]
20 CRACS & Inesc TEC [Porto]
21 Medical Center [Durham]
22 HGSC - Human Genome Sequencing Center [Houston]
23 Broad Institute [Cambridge]
24 Faculty of Medicine
25 GS - Department of Genome Sciences [Seattle]
26 454 Life Sciences [Branford]
27 National Biodefense Analysis and Countermeasures Center [Frederick]
28 CBCB - Center for Bioinformatics and Computational Biology [Maryland]
29 HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory [Hong Kong]
30 IPSO - Invariant Preserving SOlvers
31 Department of Computer Science and Software Engineering [Québec]
32 BGI - Beijing Genomics Institute [Shenzhen]
33 Berkeley California Institute for Quantitative Biosciences [Berkeley]
34 Computational Biology & Population Genomics Group [Lisboa]
35 New York Genome Center [New York]
36 Department of Molecular and Cell Biology
37 Department of Biochemistry and Biophysics
38 HHMI - Howard Hughes Medical Institute
39 Simons Center for Quantitative Biology [Cold Spring Harbor]
40 Department of Epidemiology and Biostatistics [Athens]
41 Science for Life Laboratory [Solna]
42 Department of Mathematics and Computer Science [Udine]

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.

Domaines: Architectures Matérielles [cs.AR]

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, 2013, 2 (1), pp.10. ⟨10.1186/2047-217X-2-10⟩. ⟨hal-00868822⟩