Automated ensemble assembly and validation of microbial genomes.
Automated ensemble assembly and validation of microbial genomes.
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DOI：
10.1186/1471-2105-15-126
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发表时间：
2014-05-03
影响因子：
3
通讯作者：
Phillippy AM
中科院分区：
文献类型：
--
作者：
Koren S;Treangen TJ;Hill CM;Pop M;Phillippy AM
DNA测序的持续民主化引发了基因组组装和组装验证方法的新一轮发展。随着个体研究实验室而不是集中中心开始对大多数新基因组进行测序，建立基因组组装的最佳实践非常重要。然而，最近的评估，如GAGE和组装已经得出结论，基因组组装没有单一的最佳方法。相反，最好是生成多个程序集并验证它们，以确定哪个程序集对所需的分析最有用;这是一个劳动密集型过程，通常是不可能或不可行的。为了鼓励社区支持的最佳实践，我们提出了iMetAMOS，一个自动集成装配管道; iMetAMOS封装了运行，验证和从多个组件中选择单个组件的过程。iMetAMOS将几个领先的开源工具打包成一个二进制文件，可以自动选择和执行多个汇编程序，根据多个验证指标对生成的汇编程序进行评分，并为基因和污染物的汇编程序进行注释。我们证明了225个以前未组装的结核分枝杆菌基因组以及红细菌sphaeroides基准数据集的合奏过程的效用。根据这些真实的数据，iMetAMOS可靠地生产出经过验证的组件，并在无需用户干预的情况下识别出潜在的污染。此外，智能参数选择产生R。sphaeroides的质量相当于或超过那些从GAGE-B评估，影响一些汇编程序的相对排名。使用iMetAMOS的Entrance组装为用户提供了每个基因组的多个经验证的组装。虽然计算限于小型或中型基因组，但这种方法是生成高质量组件的最有效和可重复的方法，并使用户能够选择最适合其特定需求的组件。
The continued democratization of DNA sequencing has sparked a new wave of development of genome assembly and assembly validation methods. As individual research labs, rather than centralized centers, begin to sequence the majority of new genomes, it is important to establish best practices for genome assembly. However, recent evaluations such as GAGE and the Assemblathon have concluded that there is no single best approach to genome assembly. Instead, it is preferable to generate multiple assemblies and validate them to determine which is most useful for the desired analysis; this is a labor-intensive process that is often impossible or unfeasible. To encourage best practices supported by the community, we present iMetAMOS, an automated ensemble assembly pipeline; iMetAMOS encapsulates the process of running, validating, and selecting a single assembly from multiple assemblies. iMetAMOS packages several leading open-source tools into a single binary that automates parameter selection and execution of multiple assemblers, scores the resulting assemblies based on multiple validation metrics, and annotates the assemblies for genes and contaminants. We demonstrate the utility of the ensemble process on 225 previously unassembled Mycobacterium tuberculosis genomes as well as a Rhodobacter sphaeroides benchmark dataset. On these real data, iMetAMOS reliably produces validated assemblies and identifies potential contamination without user intervention. In addition, intelligent parameter selection produces assemblies of R. sphaeroides comparable to or exceeding the quality of those from the GAGE-B evaluation, affecting the relative ranking of some assemblers. Ensemble assembly with iMetAMOS provides users with multiple, validated assemblies for each genome. Although computationally limited to small or mid-sized genomes, this approach is the most effective and reproducible means for generating high-quality assemblies and enables users to select an assembly best tailored to their specific needs.
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影响因子：
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作者：
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Goodstadt, Leo
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作者：
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