MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data.
MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data.
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DOI：
10.1371/journal.pcbi.1004957
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发表时间：
2016-06
影响因子：
4.3
通讯作者：
Tappu R
中科院分区：
文献类型：
--
作者：
Huson DH;Beier S;Flade I;Górska A;El-Hadidi M;Mitra S;Ruscheweyh HJ;Tappu R
越来越多的人对采用鸟枪测序而不是扩增子测序来分析微生物组样品感兴趣。典型的项目可能涉及数百个样品和数十亿个测序读数。将这些样品与蛋白质参考数据库进行比较会产生数十亿次比对，并且这些数据的分析在计算上具有挑战性。为了解决这个问题，我们已经大大重写和扩展了我们广泛使用的微生物组分析工具MEGAN，以促进非常大的微生物组数据集的分类和功能内容的交互式分析。其他新功能包括一个名为InterPro2GO的功能分类器，以基因为中心的读取组装，分类和功能的主坐标分析，以及对元数据的支持。这个新程序被称为MEGAN社区版（CE），是开源的。通过将MEGAN CE与我们的高通量DNA至蛋白质比对工具DIAMOND集成，并通过提供允许访问服务器上托管的宏基因组分析文件的新程序MeganServer，我们为宏基因组分析提供了一个简单、强大且完整的管道。霰弹枪序列。我们说明了如何在不到三天的时间内在一台服务器上对一个宏基因组测序项目进行全面的计算分析，该项目涉及12个样本和8亿个读数。所有源代码都可以在这里获得：https://github.com/danielhuson/megan-ce微生物组测序项目继续快速增长，无论是考虑的样本数量还是收集的测序读数。通过MEGAN社区版（CE），我们提供了一个高效的程序，用于对此类数据进行交互式分析和比较，允许人们探索数百个样本和数十亿个读数。虽然基于NCBI分类进行分类分析，但我们提供了许多不同的功能分析方法，如SEED，eggNOG，KEGG和新的InterPro2GO分类方案。MEGAN CE还支持在主坐标分析和聚类分析的上下文中使用元数据。
There is increasing interest in employing shotgun sequencing, rather than amplicon sequencing, to analyze microbiome samples. Typical projects may involve hundreds of samples and billions of sequencing reads. The comparison of such samples against a protein reference database generates billions of alignments and the analysis of such data is computationally challenging. To address this, we have substantially rewritten and extended our widely-used microbiome analysis tool MEGAN so as to facilitate the interactive analysis of the taxonomic and functional content of very large microbiome datasets. Other new features include a functional classifier called InterPro2GO, gene-centric read assembly, principal coordinate analysis of taxonomy and function, and support for metadata. The new program is called MEGAN Community Edition (CE) and is open source. By integrating MEGAN CE with our high-throughput DNA-to-protein alignment tool DIAMOND and by providing a new program MeganServer that allows access to metagenome analysis files hosted on a server, we provide a straightforward, yet powerful and complete pipeline for the analysis of metagenome shotgun sequences. We illustrate how to perform a full-scale computational analysis of a metagenomic sequencing project, involving 12 samples and 800 million reads, in less than three days on a single server. All source code is available here: https://github.com/danielhuson/megan-ce Microbiome sequencing projects continue to grow rapidly, both in the number of samples considered and sequencing reads collected. With MEGAN Community Edition (CE), we provide a highly efficient program for interactive analysis and comparison of such data, allowing one to explore hundreds of samples and billions of reads. While taxonomic profiling is performed based on the NCBI taxonomy, we provide a number of different functional profiling approaches such as SEED, eggNOG, KEGG, and a new InterPro2GO classification scheme. MEGAN CE also supports the use of metadata in the context of principal coordinate analysis and clustering analysis.