EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies.
EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies.
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DOI：
10.1093/nar/gkx967
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发表时间：
2018-01-04
影响因子：
14.9
通讯作者：
Finn RD
中科院分区：
文献类型：
--
作者：
Mitchell AL;Scheremetjew M;Denise H;Potter S;Tarkowska A;Qureshi M;Salazar GA;Pesseat S;Boland MA;Hunter FMI;Ten Hoopen P;Alako B;Amid C;Wilkinson DJ;Curtis TP;Cochrane G;Finn RD
欧洲生物信息研究所（EBI）宏基因组学平台（http://www.ebi.ac.uk/metagenomics）提供了一个免费使用的平台，用于分析和存档源自特定环境中微生物种群的序列数据。在过去两年里，EBI宏基因组学平台所分析的数据集数量增长了10倍。除了通量增加之外，基础分析流程也进行了全面革新，纳入了新的或更新的工具以及参考数据库。特别值得一提的是，一种新的分类学归类工作流程得到扩展，涵盖了基于大、小亚基RNA标记基因的归类，并囊括了所有细胞微生物。我们还介绍了将宏基因组组装作为一项新的分析服务。我们的试点研究已从公共领域的数据集生成了2400多个组装结果。基于这些组装，我们构建了一个可搜索的、包含超5000万个序列的非冗余蛋白质数据库。为了更便捷地获取该资源中存储的数据，我们开发了一个编程接口，可用于访问分析结果及相关样本元数据。最后，我们整合了一系列统计分析结果，这些结果可用于多样性估计和样本比较。
EBI metagenomics (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the analysis and archiving of sequence data derived from the microbial populations found in a particular environment. Over the past two years, EBI metagenomics has increased the number of datasets analysed 10-fold. In addition to increased throughput, the underlying analysis pipeline has been overhauled to include both new or updated tools and reference databases. Of particular note is a new workflow for taxonomic assignments that has been extended to include assignments based on both the large and small subunit RNA marker genes and to encompass all cellular micro-organisms. We also describe the addition of metagenomic assembly as a new analysis service. Our pilot studies have produced over 2400 assemblies from datasets in the public domain. From these assemblies, we have produced a searchable, non-redundant protein database of over 50 million sequences. To provide improved access to the data stored within the resource, we have developed a programmatic interface that provides access to the analysis results and associated sample metadata. Finally, we have integrated the results of a series of statistical analyses that provide estimations of diversity and sample comparisons.
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影响因子：
14.9
作者：
Cochrane G;Karsch-Mizrachi I;Takagi T;International Nucleotide Sequence Database Collaboration
通讯作者：
International Nucleotide Sequence Database Collaboration
影响因子：
64.8
作者：
Burstein D;Harrington LB;Strutt SC;Probst AJ;Anantharaman K;Thomas BC;Doudna JA;Banfield JF
通讯作者：
Banfield JF
影响因子：
14.9
作者：
Chen IA;Markowitz VM;Chu K;Palaniappan K;Szeto E;Pillay M;Ratner A;Huang J;Andersen E;Huntemann M;Varghese N;Hadjithomas M;Tennessen K;Nielsen T;Ivanova NN;Kyrpides NC
通讯作者：
Kyrpides NC
影响因子：
12.3
作者：
Chen J;Wright K;Davis JM;Jeraldo P;Marietta EV;Murray J;Nelson H;Matteson EL;Taneja V
通讯作者：
Taneja V
影响因子：
14.9
作者：
The UniProt Consortium
通讯作者：
The UniProt Consortium