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

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/ .

Keywords

Affiliated Institutions

• University of California, Berkeley US
• Cold Spring Harbor Laboratory US
• Norwich Research Park GB
• National University of Singapore SG
• Inria Rennes - Bretagne Atlantique Research Centre FR
• BGI Group (China) CN
• University of California, Davis US
• Wellcome Trust GB
• Institut de Recherche en Informatique et Systèmes Aléatoires FR
• Laboratoire d'Informatique de Paris-Nord FR
• Genome Institute of Singapore SG
• Sainsbury Laboratory GB
• Howard Hughes Medical Institute US
• Broad Institute US
• University of Georgia US
• Institut national de recherche en sciences et technologies du numérique FR
• Centre National de la Recherche Scientifique FR
• University of Maryland, College Park US
• European Bioinformatics Institute GB
• Universidade do Porto PT
• University of Chicago US
• University of California, Santa Cruz US
• Monsanto (United States) US
• Earlham Institute GB
• Iowa State University US
• BC Cancer Agency CA
• Joint Genome Institute US
• Wellcome Sanger Institute GB
• Royal Holloway University of London GB
• Institute for Systems Engineering and Computers PT
• University of California, San Francisco US
• École Normale Supérieure Paris-Saclay FR

Related Publications