Author:
Earl Dent,Bradnam Keith,St. John John,Darling Aaron,Lin Dawei,Fass Joseph,Yu Hung On Ken,Buffalo Vince,Zerbino Daniel R.,Diekhans Mark,Nguyen Ngan,Ariyaratne Pramila Nuwantha,Sung Wing-Kin,Ning Zemin,Haimel Matthias,Simpson Jared T.,Fonseca Nuno A.,Birol İnanç,Docking T. Roderick,Ho Isaac Y.,Rokhsar Daniel S.,Chikhi Rayan,Lavenier Dominique,Chapuis Guillaume,Naquin Delphine,Maillet Nicolas,Schatz Michael C.,Kelley David R.,Phillippy Adam M.,Koren Sergey,Yang Shiaw-Pyng,Wu Wei,Chou Wen-Chi,Srivastava Anuj,Shaw Timothy I.,Ruby J. Graham,Skewes-Cox Peter,Betegon Miguel,Dimon Michelle T.,Solovyev Victor,Seledtsov Igor,Kosarev Petr,Vorobyev Denis,Ramirez-Gonzalez Ricardo,Leggett Richard,MacLean Dan,Xia Fangfang,Luo Ruibang,Li Zhenyu,Xie Yinlong,Liu Binghang,Gnerre Sante,MacCallum Iain,Przybylski Dariusz,Ribeiro Filipe J.,Yin Shuangye,Sharpe Ted,Hall Giles,Kersey Paul J.,Durbin Richard,Jackman Shaun D.,Chapman Jarrod A.,Huang Xiaoqiu,DeRisi Joseph L.,Caccamo Mario,Li Yingrui,Jaffe David B.,Green Richard E.,Haussler David,Korf Ian,Paten Benedict
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/.
Publisher
Cold Spring Harbor Laboratory
Subject
Genetics(clinical),Genetics