QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data.
QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data.
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Qiime 2启用了各种微生物组数据和比较研究的全面端到端分析，并具有公开可用的数据。
DOI：
10.1002/cpbi.100
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发表时间：
2020-06
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QIIME 2是一个完全重新设计的微生物组生物信息学平台，基于流行的QIIME平台，它已经取代。QIIME 2促进了全面和完全可重现的微生物组数据科学，通过添加多个用户界面提高了对不同用户的可访问性。QIIME 2可以与开源网络平台Qiita相结合，以重新使用可用数据进行Meta分析。以下基本协议描述了如何在单台计算机上安装QIIME 2并分析微生物组序列数据，从处理原始DNA序列读数到生成可重复的交互式图形。这些交互式数字允许研究的读者与作者一样轻松地与数据进行交互，从而提高微生物组科学的透明度和可重复性。我们还展示了社区开发的用于添加分析功能的插件如何与QIIME 2一起安装和使用，从而增强微生物组分析的各个方面-例如，提高分类学分类的准确性。最后，我们说明了用户如何使用通过Qiita现成的公共数据来组合不同的数据集进行Meta分析。在本教程中，我们分析了早期儿童抗生素和微生物组（ECAM）研究的一个子集，该研究跟踪了美国43名婴儿从出生到2岁的微生物组组成和发育，确定了微生物组与抗生素暴露，分娩方式和饮食的关系。有关QIIME 2的更多信息，请参阅https://qiime2.org。要解决QIIME 2和微生物组分析的问题或提出有关QIIME 2和微生物组分析的问题，请加入活跃的社区https://forum.qiime2.org。 基本方案：使用QIIME 2和微生物组数据支持方案：进一步的微生物组分析
QIIME 2 is a completely re‐engineered microbiome bioinformatics platform based on the popular QIIME platform, which it has replaced. QIIME 2 facilitates comprehensive and fully reproducible microbiome data science, improving accessibility to diverse users by adding multiple user interfaces. QIIME 2 can be combined with Qiita, an open‐source web‐based platform, to re‐use available data for meta‐analysis. The following basic protocol describes how to install QIIME 2 on a single computer and analyze microbiome sequence data, from processing of raw DNA sequence reads through generating publishable interactive figures. These interactive figures allow readers of a study to interact with data with the same ease as its authors, advancing microbiome science transparency and reproducibility. We also show how plug‐ins developed by the community to add analysis capabilities can be installed and used with QIIME 2, enhancing various aspects of microbiome analyses—e.g., improving taxonomic classification accuracy. Finally, we illustrate how users can perform meta‐analyses combining different datasets using readily available public data through Qiita. In this tutorial, we analyze a subset of the Early Childhood Antibiotics and the Microbiome (ECAM) study, which tracked the microbiome composition and development of 43 infants in the United States from birth to 2 years of age, identifying microbiome associations with antibiotic exposure, delivery mode, and diet. For more information about QIIME 2, see https://qiime2.org. To troubleshoot or ask questions about QIIME 2 and microbiome analysis, join the active community at https://forum.qiime2.org. © 2020 The Authors. Basic Protocol: Using QIIME 2 with microbiome data Support Protocol: Further microbiome analyses