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Cold Spring Harbor Laboratory Press, Genome Research, 12(21), p. 2224-2241, 2011

DOI: 10.1101/gr.126599.111

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

Journal article published in 2011 by Dent A. Earl, Keith Bradnam ORCID, Dent A. Earl, John St. John, Aaron Darling, Dawei Lin, Joseph Fass, Hung On Ken Yu, Joseph Faas, Vince Buffalo, Daniel R. Zerbino, Hung On Ken Yu, Daniel R. Zerbino, Mark Diekhans, Ngan Nguyen and other authors.
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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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/.