Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
Authors: Bradnam Keith R , Fass Joseph N , Alexandrov Anton , Baranay Paul , Bechner Michael , Birol Inanç , Boisvert Sébastien , Chapman Jarrod A , Chapuis Guillaume , Chikhi Rayan , Chitsaz Hamidreza , Chou Wen-Chi , Corbeil Jacques , Del Fabbro Cristian , Docking T Roderick , Durbin Richard , Earl Dent , Emrich Scott , Fedotov Pavel , Fonseca Nuno A , Ganapathy Ganeshkumar , Gibbs Richard A , Gnerre Sante , Godzaridis Élénie , Goldstein Steve , Haimel Matthias , Hall Giles , Haussler David , Hiatt Joseph B , Ho Isaac Y , Howard Jason , Hunt Martin , Jackman Shaun D , Jaffe David B , Jarvis Erich D , Jiang Huaiyang , Kazakov Sergey , Kersey Paul J , Kitzman Jacob O , Knight James R , Koren Sergey , Lam Tak-Wah , Lavenier Dominique , Laviolette François , Li Yingrui , Li Zhenyu , Liu Binghang , Liu Yue , Luo Ruibang , MacCallum Iain , MacManes Matthew D , Maillet Nicolas , Melnikov Sergey , Naquin Delphine , Ning Zemin , Otto Thomas D , Paten Benedict , Paulo Octávio S , Phillippy Adam M , Pina-Martins Francisco , Place Michael , Przybylski Dariusz , Qin Xiang , Qu Carson , Ribeiro Filipe J , Richards Stephen , Rokhsar Daniel S , Ruby J Graham , Scalabrin Simone , Schatz Michael C , Schwartz David C , Sergushichev Alexey , Sharpe Ted , Shaw Timothy I , Shendure Jay , Shi Yujian , Simpson Jared T , Song Henry , Tsarev Fedor , Vezzi Francesco , Vicedomini Riccardo , Vieira Bruno M , Wang Jun , Worley Kim C , Yin Shuangye , Yiu Siu-Ming , Yuan Jianying , Zhang Guojie , Zhang Hao , Zhou Shiguo , Korf Ian F 
Published: July 2013

Abstract

Background
The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly.

Results
In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies.

Conclusions
Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.