Campus Units

Computer Science

Document Type

Article

Publication Version

Published Version

Publication Date

2011

Journal or Book Title

Genome Research

Volume

21

First Page

2224

Last Page

2241

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/.

Comments

This article is published as Earl, Dent A., Keith Bradnam, John St John, Aaron Darling, Dawei Lin, Joseph Faas, Hung On Ken Yu et al. "Assemblathon 1: a competitive assessment of de novo short read assembly methods." Genome research 21 (2011): 2224-2241. doi: 10.1101/gr.126599.111.

Rights

Works produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The content of this document is not copyrighted.

Language

en

File Format

application/pdf

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