利用系统发育放置进行宏基因组分析——第一个十年综述
Metagenomic Analysis using Phylogenetic Placement -- A Review of the First Decade
AI总结：
本文综述系统发育放置十年发展，梳理其从原始序列到结果可视化的完整流程、常用工具、典型下游分析、最佳实践及常见误区。
摘要：
系统发育放置（phylogenetic placement）是指一类工具和方法，用于分析、可视化和解释由高通量测序产生的海量宏基因组测序数据。与其他方法（例如基于相似性的方法）相比，它利用一组已知参考序列，并将进化历史纳入考虑，从而把宏条形码序列置于系统发育背景之中。由此，人们可以提高宏基因组调查的准确性，并消除必须与现有序列数据库存在精确或近似匹配的要求。系统发育放置本身就是一种有价值的分析工具，同时还伴随大量用于解释其结果的下游工具。一个常见应用场景是分析通过宏基因组测序获得的物种群落，例如通过分类学归属、多样性量化、样本比较以及识别与环境变量之间的相关性。在本综述中，我们概述了第一个十年间发展起来的方法。具体而言，本综述的目标是：（i）说明使用系统发育放置的动机并展示其部分应用场景；（ii）勾勒从原始序列到可发表图表的完整工作流程，包括最佳实践；（iii）介绍最常见的工具和方法及其能力；（iv）指出常见的放置陷阱和误解；（v）展示典型的基于放置的分析，以及它们如何帮助分析、可视化和解释系统发育放置数据。
英文摘要：
Phylogenetic placement refers to a family of tools and methods to analyze, visualize, and interpret the tsunami of metagenomic sequencing data generated by high-throughput sequencing. Compared to alternative (e. g., similarity-based) methods, it puts metabarcoding sequences into a phylogenetic context using a set of known reference sequences and taking evolutionary history into account. Thereby, one can increase the accuracy of metagenomic surveys and eliminate the requirement for having exact or close matches with existing sequence databases. Phylogenetic placement constitutes a valuable analysis tool per se, but also entails a plethora of downstream tools to interpret its results. A common use case is to analyze species communities obtained from metagenomic sequencing, for example via taxonomic assignment, diversity quantification, sample comparison, and identification of correlations with environmental variables. In this review, we provide an overview over the methods developed during the first ten years. In particular, the goals of this review are (i) to motivate the usage of phylogenetic placement and illustrate some of its use cases, (ii) to outline the full workflow, from raw sequences to publishable figures, including best practices, (iii) to introduce the most common tools and methods and their capabilities, (iv) to point out common placement pitfalls and misconceptions,(v) to showcase typical placement-based analyses, and how they can help to analyze, visualize, and interpret phylogenetic placement data.
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
