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

Bradnam, Keith R., Fass, Joseph N., Alexandrov, Anton, Baranay, Paul, Bechner, Michael, Birol, Inanc, Boisvert, Sebastien, Chapman, Jarrod A., Chapuis, Guillaume, Chikhi, Rayan, Chitsaz, Hamidreza, Chou, Wen-Chi, Corbeil, Jacques, Del Fabbro, Cristian, Docking, T. Roderick, Durbin, Richard, Earl, Dent, Emrich, Scott, Fedotov, Pavel, Fonseca, Nuno A., Ganapathy, Ganeshkumar, Gibbs, Richard A., Gnerre, Sante, Godzaridis, Elenie, Goldstein, Steve, Haimel, Matthias, Hall, Giles, Haussler, David, Hiatt, Joseph B., Ho, Isaac Y., Howard, Jason, Hunt, Martin, Jackman, Shaun D., Jaffe, David B., Jarvis, Erich D., Jiang, Huaiyang, Kazakov, Sergey, Kersey, Paul J., Kitzman, Jacob O., Knight, James R., Koren, Sergey, Lam, Tak-Wah, Lavenier, Dominique, Laviolette, Francois, Li, Yingrui, Li, Zhenyu, Liu, Binghang, Liu, Yue, Luo, Ruibang, MacCallum, Iain, MacManes, Matthew D., Maillet, Nicolas, Melnikov, Sergey, Naquin, Delphine, Ning, Zemin, Otto, Thomas D., Paten, Benedict, Paulo, Octavio S., Phillippy, Adam M., Pina-Martins, Francisco, Place, Michael, Przybylski, Dariusz, Qin, Xiang, Qu, Carson, Ribeiro, Filipe J., Richards, Stephen, Rokhsar, Daniel S., Ruby, J. Graham, Scalabrin, Simone, Schatz, Michael C., Schwartz, David C., Sergushichev, Alexey, Sharpe, Ted, Shaw, Timothy I., Shendure, Jay, Shi, Yujian, Simpson, Jared T., Song, Henry, Tsarev, Fedor, Vezzi, Francesco, Vicedomini, Riccardo, Vieira, Bruno M., Wang, Jun, Worley, Kim C., Yin, Shuangye, Yiu, Siu-Ming, Yuan, Jianying, Zhang, Guojie, Zhang, Hao, Zhou, Shiguo and Korf, Ian F. (2013) Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience, 2 1: . doi:10.1186/2047-217X-2-10

Author Bradnam, Keith R.
Fass, Joseph N.
Alexandrov, Anton
Baranay, Paul
Bechner, Michael
Birol, Inanc
Boisvert, Sebastien
Chapman, Jarrod A.
Chapuis, Guillaume
Chikhi, Rayan
Chitsaz, Hamidreza
Chou, Wen-Chi
Corbeil, Jacques
Del Fabbro, Cristian
Docking, T. Roderick
Durbin, Richard
Earl, Dent
Emrich, Scott
Fedotov, Pavel
Fonseca, Nuno A.
Ganapathy, Ganeshkumar
Gibbs, Richard A.
Gnerre, Sante
Godzaridis, Elenie
Goldstein, Steve
Haimel, Matthias
Hall, Giles
Haussler, David
Hiatt, Joseph B.
Ho, Isaac Y.
Howard, Jason
Hunt, Martin
Jackman, Shaun D.
Jaffe, David B.
Jarvis, Erich D.
Jiang, Huaiyang
Kazakov, Sergey
Kersey, Paul J.
Kitzman, Jacob O.
Knight, James R.
Koren, Sergey
Lam, Tak-Wah
Lavenier, Dominique
Laviolette, Francois
Li, Yingrui
Li, Zhenyu
Liu, Binghang
Liu, Yue
Luo, Ruibang
MacCallum, Iain
MacManes, Matthew D.
Maillet, Nicolas
Melnikov, Sergey
Naquin, Delphine
Ning, Zemin
Otto, Thomas D.
Paten, Benedict
Paulo, Octavio S.
Phillippy, Adam M.
Pina-Martins, Francisco
Place, Michael
Przybylski, Dariusz
Qin, Xiang
Qu, Carson
Ribeiro, Filipe J.
Richards, Stephen
Rokhsar, Daniel S.
Ruby, J. Graham
Scalabrin, Simone
Schatz, Michael C.
Schwartz, David C.
Sergushichev, Alexey
Sharpe, Ted
Shaw, Timothy I.
Shendure, Jay
Shi, Yujian
Simpson, Jared T.
Song, Henry
Tsarev, Fedor
Vezzi, Francesco
Vicedomini, Riccardo
Vieira, Bruno M.
Wang, Jun
Worley, Kim C.
Yin, Shuangye
Yiu, Siu-Ming
Yuan, Jianying
Zhang, Guojie
Zhang, Hao
Zhou, Shiguo
Korf, Ian F.
Title Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
Formatted title
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
Journal name Gigascience   Check publisher's open access policy
ISSN 2047-217X
Publication date 2013-07-22
Sub-type Article (original research)
DOI 10.1186/2047-217X-2-10
Open Access Status DOI
Volume 2
Issue 1
Total pages 31
Place of publication London, United Kingdom
Publisher BioMed Central
Language eng
Formatted 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.
Keyword Genome assembly
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ
Additional Notes Article number 10

Document type: Journal Article
Sub-type: Article (original research)
Collection: Institute for Molecular Bioscience - Publications
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