iMAP：用于微生物组数据分析的集成生物信息学和可视化管道。

BACKGROUND: One of the major challenges facing investigators in the microbiome field is turning large numbers of reads generated by next-generation sequencing (NGS) platforms into biological knowledge. Effective analytical workflows that guarantee reproducibility, repeatability, and result provenance are essential requirements of modern microbiome research. For nearly a decade, several state-of-the-art bioinformatics tools have been developed for understanding microbial communities living in a given sample. However, most of these tools are built with many functions that require an in-depth understanding of their implementation and the choice of additional tools for visualizing the final output. Furthermore, microbiome analysis can be time-consuming and may even require more advanced programming skills which some investigators may be lacking. RESULTS: We have developed a wrapper named iMAP (Integrated Microbiome Analysis Pipeline) to provide the microbiome research community with a user-friendly and portable tool that integrates bioinformatics analysis and data visualization. The iMAP tool wraps functionalities for metadata profiling, quality control of reads, sequence processing and classification, and diversity analysis of operational taxonomic units. This pipeline is also capable of generating web-based progress reports for enhancing an approach referred to as review-as-you-go (RAYG). For the most part, the profiling of microbial community is done using functionalities implemented in Mothur or QIIME2 platform. Also, it uses different R packages for graphics and R-markdown for generating progress reports. We have used a case study to demonstrate the application of the iMAP pipeline. CONCLUSIONS: The iMAP pipeline integrates several functionalities for better identification of microbial communities present in a given sample. The pipeline performs in-depth quality control that guarantees high-quality results and accurate conclusions. The vibrant visuals produced by the pipeline facilitate a better understanding of the complex and multidimensional microbiome data. The integrated RAYG approach enables the generation of web-based reports, which provides the investigators with the intermediate output that can be reviewed progressively. The intensively analyzed case study set a model for microbiome data analysis.

背景：下一代测序（NGS）平台产生的大量reads 给微生物组领域的研究人员带来了巨大的挑战，他们需要将这些数据转化为有意义的生物学知识。可重复、可重现且可追溯的有效分析工作流程是现代微生物组研究的基本要求。近十年来，已经开发了许多用于理解特定样本中微生物群落的先进生物信息学工具。然而，这些工具中的大多数都具有许多功能，这需要深入了解其实现以及选择其他工具来可视化最终输出。此外，微生物组分析可能很耗时，甚至可能需要一些研究人员所缺乏的更高级的编程技能。

结果：我们开发了一个名为 iMAP（Integrated Microbiome Analysis Pipeline）的包装器，为微生物组研究社区提供了一个用户友好且可移植的工具，它集成了生物信息学分析和数据可视化功能。iMAP 工具包装了元数据分析、reads 质量控制、序列处理和分类以及操作分类单元多样性分析的功能。该管道还能够生成基于网络的进度报告，以增强所谓的“边做边审（review-as-you-go，RAYG）”方法。在大多数情况下，微生物群落的分析是使用 Mothur 或 QIIME2 平台实现的功能完成的。此外，它还使用不同的 R 包进行图形处理和 R 标记以生成进度报告。我们使用一个案例研究来说明 iMAP 管道的应用。

结论：iMAP 管道集成了多个功能，可更好地识别给定样本中存在的微生物群落。该管道执行深度质量控制，可确保高质量的结果和准确的结论。该管道生成的生动可视化效果有助于更好地理解复杂的多维微生物组数据。集成的 RAYG 方法可生成基于网络的报告，为研究人员提供可逐步审查的中间输出。经过深入分析的案例研究为微生物组数据分析树立了一个模型。