Archive

  • Visit JGI.DOE.GOV
News & Publications
Home › Publications › Assemblathon 1: a competitive assessment of de novo short read assembly methods

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

Published in:

Genome Res 21(12) , 2224-41 (Dec 2011)

Author(s):

Earl, D., Bradnam, K., St John, J., Darling, A., Lin, D., Fass, J., Yu, H. O., Buffalo, V., Zerbino, D. R., Diekhans, M., Nguyen, N., Ariyaratne, P. N., Sung, W. K., Ning, Z., Haimel, M., Simpson, J. T., Fonseca, N. A., Birol, I., Docking, T. R., Ho, I. Y., Rokhsar, D. S., Chikhi, R., Lavenier, D., Chapuis, G., Naquin, D., Maillet, N., Schatz, M. C., Kelley, D. R., Phillippy, A. M., Koren, S., Yang, S. P., Wu, W., Chou, W. C., Srivastava, A., Shaw, T. I., Ruby, J. G., Skewes-Cox, P., Betegon, M., Dimon, M. T., Solovyev, V., Seledtsov, I., Kosarev, P., Vorobyev, D., Ramirez-Gonzalez, R., Leggett, R., MacLean, D., Xia, F., Luo, R., Li, Z., Xie, Y., Liu, B., Gnerre, S., MacCallum, I., Przybylski, D., Ribeiro, F. J., Yin, S., Sharpe, T., Hall, G., Kersey, P. J., Durbin, R., Jackman, S. D., Chapman, J. A., Huang, X., DeRisi, J. L., Caccamo, M., Li, Y., Jaffe, D. B., Green, R. E., Haussler, D., Korf, I., Paten, B.

DOI:

10.1101/gr.126599.111

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 http://www.assemblathon.org/.

View Publication

Share this:

  • Click to share on Facebook (Opens in new window)
  • Click to share on LinkedIn (Opens in new window)
  • Click to share on Pinterest (Opens in new window)
  • Click to share on Twitter (Opens in new window)
  • Click to print (Opens in new window)
  • JGI.DOE.GOV
  • Disclaimer
  • Accessibility / Section 508
Lawrence Berkeley National Lab Biosciences Area
A project of the US Department of Energy, Office of Science

JGI is a DOE Office of Science User Facility managed by Lawrence Berkeley National Laboratory

© 1997-2025 The Regents of the University of California