Huson Daniel H, Weber Nico
Center for Bioinformatics, University of Tübingen, Tübingen, Germany.
Methods Enzymol. 2013;531:465-85. doi: 10.1016/B978-0-12-407863-5.00021-6.
Metagenomics, the study of microbes in the environment using DNA sequencing, depends upon dedicated software tools for processing and analyzing very large sequencing datasets. One such tool is MEGAN (MEtaGenome ANalyzer), which can be used to interactively analyze and compare metagenomic and metatranscriptomic data, both taxonomically and functionally. To perform a taxonomic analysis, the program places the reads onto the NCBI taxonomy, while functional analysis is performed by mapping reads to the SEED, COG, and KEGG classifications. Samples can be compared taxonomically and functionally, using a wide range of different charting and visualization techniques. PCoA analysis and clustering methods allow high-level comparison of large numbers of samples. Different attributes of the samples can be captured and used within analysis. The program supports various input formats for loading data and can export analysis results in different text-based and graphical formats. The program is designed to work with very large samples containing many millions of reads. It is written in Java and installers for the three major computer operating systems are available from http://www-ab.informatik.uni-tuebingen.de.
宏基因组学是利用DNA测序技术对环境中的微生物进行研究，它依赖于专门的软件工具来处理和分析非常大的测序数据集。其中一个工具是MEGAN（宏基因组分析器），它可用于从分类学和功能方面交互式地分析和比较宏基因组学和宏转录组学数据。为了进行分类学分析，该程序将读段定位到NCBI分类法上，而功能分析则通过将读段映射到SEED、COG和KEGG分类来进行。可以使用各种不同的图表和可视化技术，从分类学和功能方面对样本进行比较。主坐标分析（PCoA）和聚类方法允许对大量样本进行高层次比较。在分析过程中可以获取并使用样本的不同属性。该程序支持多种用于加载数据的输入格式，并能以不同的基于文本和图形的格式导出分析结果。该程序设计用于处理包含数百万读段的非常大的样本。它用Java编写，可从http://www-ab.informatik.uni-tuebingen.de获得适用于三大计算机操作系统的安装程序。
