Assemblathon 2：三种脊椎动物物种中基因组从头组装方法的评估
摘要
背景 - 生成原始基因组序列数据的过程正变得愈发廉价、快速且准确。然而，将此类数据组装为高质量的完成基因组序列仍具挑战性。目前已有许多基因组组装工具可用，但它们在性能（速度、可扩展性、硬件要求、对新型测序技术的兼容性）和最终输出（组装序列的组成）方面差异巨大。更重要的是，目前仍不清楚如何最好地评估组装基因组序列的质量。Assemblathon 竞赛旨在评估当前基因组组装领域的最先进方法。结果 - 在 Assemblathon 2 中，我们提供了三种脊椎动物物种（一种鸟类、一种鱼类和一种蛇类）的多种待组装序列数据。这最终促成了来自 21 个参赛团队的共 43 份提交组装结果。我们结合光学图谱数据、Fosmid 序列和多种统计方法对这些组装结果进行了评估。从超过 100 项不同的指标中，我们选取了十项关键指标来评估组装结果的整体质量。结论 - 许多当前的基因组组装器产生了有用的组装结果，包含对其基因、调控序列和整体基因组结构的显著表征。然而，各条目之间的高度变异性表明，基因组组装领域仍有很大的改进空间，且在一种物种基因组组装中表现良好的方法未必适用于另一种物种。
引用
@article{arxiv.1301.5406,
title = {Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species},
author = {Keith R. Bradnam and Joseph N. Fass and Anton Alexandrov and Paul Baranay and Michael Bechner and İnanç Birol and Sébastien Boisvert and Jarrod A. Chapman and Guillaume Chapuis and Rayan Chikhi and Hamidreza Chitsaz and Wen-Chi Chou and Jacques Corbeil and Cristian Del Fabbro and T. Roderick Docking and Richard Durbin and Dent Earl and Scott Emrich and Pavel Fedotov and Nuno A. Fonseca and Ganeshkumar Ganapathy and Richard A. Gibbs and Sante Gnerre and Élénie Godzaridis and Steve Goldstein and Matthias Haimel and Giles Hall and David Haussler and Joseph B. Hiatt and Isaac Y. Ho and Jason Howard and Martin Hunt and Shaun D. Jackman and David B Jaffe and Erich Jarvis and Huaiyang Jiang and Sergey Kazakov and Paul J. Kersey and Jacob O. Kitzman and James R. Knight and Sergey Koren and Tak-Wah Lam and Dominique Lavenier and François Laviolette and Yingrui Li and Zhenyu Li and Binghang Liu and Yue Liu and Ruibang Luo and Iain MacCallum and Matthew D MacManes and Nicolas Maillet and Sergey Melnikov and Bruno Miguel Vieira and Delphine Naquin and Zemin Ning and Thomas D. Otto and Benedict Paten and Octávio S. Paulo and Adam M. Phillippy and Francisco Pina-Martins and Michael Place and Dariusz Przybylski and Xiang Qin and Carson Qu and Filipe J Ribeiro and Stephen Richards and Daniel S. Rokhsar and J. Graham Ruby and Simone Scalabrin and Michael C. Schatz and David C. Schwartz and Alexey Sergushichev and Ted Sharpe and Timothy I. Shaw and Jay Shendure and Yujian Shi and Jared T. Simpson and Henry Song and Fedor Tsarev and Francesco Vezzi and Riccardo Vicedomini and Jun Wang and Kim C. Worley and Shuangye Yin and Siu-Ming Yiu and Jianying Yuan and Guojie Zhang and Hao Zhang and Shiguo Zhou and Ian F. Korf},
journal= {arXiv preprint arXiv:1301.5406},
year = {2015}
}
备注
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, & Experiment identifiers 3. Made miscellaneous changes to address reviewers comments. DOIs added to GigaDB datasets