Assemblathon 1: A competitive assessment of de novo short read assembly methods

Dent A. Earl (1, 2) , Keith Bradnam (3) , John St. John (1, 2) , Aaron Darling (3) , Dawei Lin (3, 4) , Joseph Faas (3, 4) , Hung On Ken Yu (3) , Buffalo Vince (3, 4) , Daniel R. Zerbino (2) , Mark Diekhans (2, 1) , Ngan Nguyen (1, 2) , Pramila Nuwantha (5) , Ariyaratne Wing-Kin Sung (5, 6) , Zemin Ning (7) , Matthias Haimel (8) , Jared T. Simpson (7) , Nuno A. Fronseca (9) , Inanç Birol (10) , T. Roderick Docking (10) , Isaac Y. Ho (11) , Daniel S Rokhsar (11, 12) , Rayan Chikhi (13) , Dominique Lavenier (13) , Guillaume Chapuis (13) , Delphine Naquin (13) , Nicolas Maillet (13) , Michael C. Schatz (14) , David R. Kelly (15) , Adam M. Phillippy (15, 16) , Sergey Koren (15, 16) , Shiaw-Pyng Yang (17) , Wei Wu (17) , Wen-Chi Chou (18) , Anuj Srivastava (18) , Timothy I. Shaw (18) , J. Graham Ruby (19, 20) , Peter Skewes-Cox (20, 19, 21) , Miguel Betegon (20, 19) , Michelle T. Dimon (20, 19) , Victor Solovyev (22) , Petr Kosarev (23) , Denis Vorobyev (23) , Ricardo Ramirez-Gonzalez (24) , Richard Leggett (25) , Dan Maclean (25) , Fangfang Xia (26) , Ruibang Luo (27) , Zhenyu Li (27) , Yinlong Xie (27) , Binghang Liu (27) , Sante Gnerre (28) , Iain Maccallum (28) , Dariusz Przybylski (28) , Filipe J. Ribeiro (28) , Shuangye Yin (28) , Ted Sharpe (28) , Giles Hall (28) , Paul J. Kersey (8) , Richard Durbin (7) , Shaun D. Jackman (10) , Jarrod A. Chapman (11) , Xiaoqiu Huang (29) , Joseph L. Derisi (19, 21) , Mario Caccamo (24) , Yingrui Li (27) , David B. Jaffe (28) , Richard M. Green (2) , David Haussler (1, 2, 19) , Ian Korf (3) , Benedict Paten (1, 2, 19)

1 Center for Biomolecular Science and Engineering
2 Biomolecular Engineering Department
3 Genome Center [UC Davis]
4 UC Davis - Bioinformatics Core [Univ California Davis]
5 Computational and Mathematical Biology
6 NUS - School of computing [Singapore]
7 The Wellcome Trust Sanger Institute [Cambridge]
8 EMBL-EBI - European Bioinformatics Institute [Hinxton]
9 CRACS INESC - Center for Research in Advanced Computing Systems
10 GSC - Genome Sciences Centre [Vancouver]
11 DOE Joint Genome Institute [Walnut Creek]
12 Department of Molecular & Cell Biology [Berkeley]
13 SYMBIOSE - Biological systems and models, bioinformatics and sequences
14 Simons Center for Quantitative Biology [Cold Spring Harbor]
15 CBCB - Center for Bioinformatics and Computational Biology [Maryland]
16 National Biodefense Analysis and Countermeasures Center [Frederick]
17 Monsanto Company
18 IOB - Institute of Bioinformatics [Georgia]
19 HHMI - Howard Hughes Medical Institute [Chevy Chase]
20 Department of Biochemistry and Biophysics [San Francisco]
21 BMI - Biological and Medical Informatics [San Francisco]
22 Department of Computer Science [Royal Holloway]
23 Softberry Inc
24 TGAC - The Genome Analysis Centre
25 SLCU - Sainsbury Laboratory Cambridge University
26 Computation Institute [Chicago]
27 BGI - Beijing Genomics Institute [Shenzhen]
28 Broad Institute [Cambridge]
29 Department of Computer Science [Ames]

Low cost short read sequencing technology has revolutionised genomics, though it is only just becoming practical for the high quality de novo assembly of a novel large genome. We describe the Assemblathon 1 competition, which aimed to comprehensively assess the state of the art in de novo assembly methods when applied to current sequencing technologies. In a collaborative effort teams were asked to assemble a simulated Illumina HiSeq dataset of an unknown, simulated diploid genome. A total of 41 assemblies from 17 different groups were received. Novel haplotype aware assessments of coverage, contiguity, structure, base calling and copy number were made. We establish that within this benchmark (1) it is possible to assemble the genome to a high level of coverage and accuracy, and that (2) large differences exist between the assemblies, suggesting room for further improvements in current methods.

Domaines: Bio-informatique [q-bio.QM]; Bio-Informatique, Biologie Systémique [q-bio.QM]

Dent A. Earl, Keith Bradnam, John St. John, Aaron Darling, Dawei Lin, et al.. Assemblathon 1: A competitive assessment of de novo short read assembly methods. Genome Research, 2011, ⟨10.1101/gr.126599.111⟩. ⟨inria-00637571⟩