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

description: 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, regulatory sequences, 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.
description: Additional files available at http://korflab.ucdavis.edu/Datasets/Assemblathon/Assemblathon2/Additional_files/ Major changes 1. Accessions for the 3 read data sets have now been included 2. New file: spreadsheet containing details of all Study, Sample, Run, &amp; Experiment identifiers 3. Made miscellaneous changes to address reviewers comments. DOIs added to GigaDB datasets