MGnify: the microbiome analysis resource in 2020
MGnify: the microbiome analysis resource in 2020
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DOI：
10.1093/nar/gkz1035
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发表时间：
2020-01-08
影响因子：
14.9
通讯作者：
Finn, Robert D.
中科院分区：
文献类型：
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作者：
Mitchell, Alex L.;Almeida, Alexandre;Finn, Robert D.
MGnify （http://www.ebi.ac.uk/metagenomics）提供了一个免费使用的平台，用于组装，分析和存档来自特定环境中存在的微生物种群测序的微生物组数据。在过去的两年中，MGnify（前身为EBI Metagenomics）已将资源中持有的公开可用分析数据集的数量增加了一倍以上。最近，一种更新的数据分析方法已经公布（版本5.0），用根据输入数据定制的多个分析管道取代了以前的单个管道，并使用公共工作流语言进行正式描述，从而实现了更好的来源、可重用性和可再现性。MGnify的新分析管道为基于核糖体内部转录间隔区（ITS1/2）和扩展的蛋白质功能注释的分类断言提供了额外的方法。生化途径和系统预测也被添加到组装的contigs。magnify对宏基因组数据组装的日益关注也使其组装和分析的数据集数量增加了六倍。由这些组合编码的蛋白质构建的非冗余蛋白质数据库现在超过10亿个序列。同时，新开发的配置查看器提供了组装的配置及其丰富注释的细粒度可视化。
MGnify ( http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline with multiple analysis pipelines that are tailored according to the input data, and that are formally described using the Common Workflow Language, enabling greater provenance, reusability, and reproducibility. MGnify's new analysis pipelines offer additional approaches for taxonomic assertions based on ribosomal internal transcribed spacer regions (ITS1/2) and expanded protein functional annotations. Biochemical pathways and systems predictions have also been added for assembled contigs. MGnify's growing focus on the assembly of metagenomic data has also seen the number of datasets it has assembled and analysed increase six-fold. The non-redundant protein database constructed from the proteins encoded by these assemblies now exceeds 1 billion sequences. Meanwhile, a newly developed contig viewer provides fine-grained visualisation of the assembled contigs and their enriched annotations.