July 7, 2019  |  

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

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

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.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.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.

Journal: GigaScience
DOI: 10.1186/2047-217X-2-10
Year: 2013

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