Assemblathon 1: A competitive assessment of de novo short read assembly methods
Assemblathon 1: A competitive assessment of de novo short read assembly methods
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DOI：
10.1101/gr.126599.111
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发表时间：
2011-12-01
期刊：
影响因子：
7
通讯作者：
Paten, Benedict
中科院分区：
文献类型：
--
作者：
Earl, Dent;Bradnam, Keith;Paten, Benedict
低成本的短读测序技术已经给基因组学带来了革命性的变化，尽管它对于高质量的新的大基因组的从头组装才刚刚开始实用。我们描述了第一次装配大赛，它的目的是全面评估应用于当前测序技术的从头组装方法的最新水平。在一项合作工作中，团队被要求组装一个未知的模拟二倍体基因组的模拟Illumina HiSeq数据集。总共收到了来自17个不同团体的41个集会。对覆盖率、邻接性、结构、碱基调用和拷贝数进行了新的单倍型感知评估。在这一基准下，我们确定：(1)有可能以高水平的覆盖率和准确性组装基因组，(2)组装之间存在巨大差异，这表明当前方法有进一步改进的空间。包括正确答案、程序集和用于评估程序集的代码在内的模拟基准现在是公开的，可以从http://www.assemblathon.org/.免费获得
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/.