The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes
The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes
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DOI：
10.1186/1471-2105-9-386
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发表时间：
2008-09-19
影响因子：
3
通讯作者：
Edwards, R. A.
中科院分区：
文献类型：
--
作者：
Meyer, F.;Paarmann, D.;Edwards, R. A.
背景：随机群落基因组（宏基因组）现在通常用于研究不同环境中的微生物。在过去几年中，与宏基因组学相关的主要挑战从生成序列转移到了分析序列。高通量、低成本的新一代测序使众多研究人员能够进行宏基因组学研究。
结果：构建了一个高通量流程，为所有有兴趣使用宏基因组学的研究人员提供高性能计算。该流程通过比较蛋白质和核苷酸数据库，对宏基因组中的序列进行自动功能注释。生成宏基因组的系统发育和功能概要，并将比较宏基因组学的工具纳入标准视图。用户访问受到控制以确保数据隐私，但支撑该服务的协作环境为多个用户之间共享数据集提供了框架。在宏基因组学RAST中，所有用户都完全掌控自己的数据，并且所有数据都可以多种格式下载。
结论：开源的宏基因组学RAST服务为宏基因组的注释和分析提供了一种新模式。宏基因组学RAST具有对多种数据源的内置支持以及容纳抽象数据类型的后端，它稳定、可扩展，并且所有研究人员均可免费使用。该服务消除了宏基因组序列分析中的一个主要瓶颈——用于注释数据的高性能计算的可用性。
Background: Random community genomes (metagenomes) are now commonly used to study microbes in different environments. Over the past few years, the major challenge associated with metagenomics shifted from generating to analyzing sequences. High-throughput, low-cost next-generation sequencing has provided access to metagenomics to a wide range of researchers.Results: A high-throughput pipeline has been constructed to provide high-performance computing to all researchers interested in using metagenomics. The pipeline produces automated functional assignments of sequences in the metagenome by comparing both protein and nucleotide databases. Phylogenetic and functional summaries of the metagenomes are generated, and tools for comparative metagenomics are incorporated into the standard views. User access is controlled to ensure data privacy, but the collaborative environment underpinning the service provides a framework for sharing datasets between multiple users. In the metagenomics RAST, all users retain full control of their data, and everything is available for download in a variety of formats.Conclusion: The open-source metagenomics RAST service provides a new paradigm for the annotation and analysis of metagenomes. With built-in support for multiple data sources and a back end that houses abstract data types, the metagenomics RAST is stable, extensible, and freely available to all researchers. This service has removed one of the primary bottlenecks in metagenome sequence analysis-the availability of high-performance computing for annotating the data.