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

Earl, Dent, Bradnam, Keith, St John, John, Darling, Aaron, Lin, Dawei, Fass, Joseph, Hung On Ken Yu, Buffalo, Vince, Zerbino, Daniel R., Diekhans, Mark, Ngan Nguyen, Ariyaratne, Pramila Nuwantha, Sung, Wing-Kin, Ning, Zemin, Haimel, Matthias, Simpson, Jared T., Fonseca, Nuno A., Birol, Inanc, Docking, T. Roderick, Ho, Isaac Y., Rokhsar, Daniel S., Chikhi, Rayan, Lavenier, Dominique, Chapuis, Guillaume, Naquin, Delphine, Maillet, Nicolas, Schatz, Michael C., Kelley, David R., Phillippy, Adam M., Koren, Sergey, Yang, Shiaw-Pyng, Wu, Wei, Chou, Wen-Chi, Srivastava, Anuj, Shaw, Timothy I., Ruby, J. Graham, Skewes-Cox, Peter, Betegon, Miguel, Dimon, Michelle T., Solovyev, Victor, Seledtsov, Igor, Kosarev, Petr, Vorobyev, Denis, Ramirez-Gonzalez, Ricardo, Leggett, Richard, MacLean, Dan, Xia, Fangfang, Luo, Ruibang, Li, Zhenyu, Xie, Yinlong, Liu, Binghang, Gnerre, Sante, MacCallum, Iain, Przybylski, Dariusz, Ribeiro, Filipe J., Yin, Shuangye, Sharpe, Ted, Hall, Giles, Kersey, Paul J., Durbin, Richard, Jackman, Shaun D., Chapman, Jarrod A., Huang, Xiaoqiu, DeRisi, Joseph L., Caccamo, Mario, Li, Yingrui, Jaffe, David B., Green, Richard E., Haussler, David, Korf, Ian and Paten, Benedict (2011) Assemblathon 1: A competitive assessment of de novo short read assembly methods. Genome Research, 21 12: 2224-2241. doi:10.1101/gr.126599.111

Author Earl, Dent
Bradnam, Keith
St John, John
Darling, Aaron
Lin, Dawei
Fass, Joseph
Hung On Ken Yu
Buffalo, Vince
Zerbino, Daniel R.
Diekhans, Mark
Ngan Nguyen
Ariyaratne, Pramila Nuwantha
Sung, Wing-Kin
Ning, Zemin
Haimel, Matthias
Simpson, Jared T.
Fonseca, Nuno A.
Birol, Inanc
Docking, T. Roderick
Ho, Isaac Y.
Rokhsar, Daniel S.
Chikhi, Rayan
Lavenier, Dominique
Chapuis, Guillaume
Naquin, Delphine
Maillet, Nicolas
Schatz, Michael C.
Kelley, David R.
Phillippy, Adam M.
Koren, Sergey
Yang, Shiaw-Pyng
Wu, Wei
Chou, Wen-Chi
Srivastava, Anuj
Shaw, Timothy I.
Ruby, J. Graham
Skewes-Cox, Peter
Betegon, Miguel
Dimon, Michelle T.
Solovyev, Victor
Seledtsov, Igor
Kosarev, Petr
Vorobyev, Denis
Ramirez-Gonzalez, Ricardo
Leggett, Richard
MacLean, Dan
Xia, Fangfang
Luo, Ruibang
Li, Zhenyu
Xie, Yinlong
Liu, Binghang
Gnerre, Sante
MacCallum, Iain
Przybylski, Dariusz
Ribeiro, Filipe J.
Yin, Shuangye
Sharpe, Ted
Hall, Giles
Kersey, Paul J.
Durbin, Richard
Jackman, Shaun D.
Chapman, Jarrod A.
Huang, Xiaoqiu
DeRisi, Joseph L.
Caccamo, Mario
Li, Yingrui
Jaffe, David B.
Green, Richard E.
Haussler, David
Korf, Ian
Paten, Benedict
Title Assemblathon 1: A competitive assessment of de novo short read assembly methods
Journal name Genome Research   Check publisher's open access policy
ISSN 1088-9051
Publication date 2011-09-16
Sub-type Critical review of research, literature review, critical commentary
DOI 10.1101/gr.126599.111
Open Access Status DOI
Volume 21
Issue 12
Start page 2224
End page 2241
Total pages 18
Place of publication Cold Spring Harbor, NY, United States
Publisher Cold Spring Harbor Laboratory Press
Language eng
Abstract Low-cost short read sequencing technology has revolutionized 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 data set 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. The simulated benchmark, including the correct answer, the assemblies, and the code that was used to evaluate the assemblies is now public and freely available from
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Critical review of research, literature review, critical commentary
Collection: Institute for Molecular Bioscience - Publications
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