论文标题

使用系统发育放置的宏基因组学分析 - 最初十年的回顾

Metagenomic Analysis using Phylogenetic Placement -- A Review of the First Decade

论文作者

Czech, Lucas, Stamatakis, Alexandros, Dunthorn, Micah, Barbera, Pierre

论文摘要

系统发育放置是指一系列工具和方法,用于分析,可视化和解释高通量测序产生的元基因组测序数据的海啸。与替代方法(例如基于相似性的方法)相比,它使用一组已知参考序列并考虑了进化史将元编码序列置于系统发育环境中。因此,可以提高宏基因组调查的准确性,并消除与现有序列数据库具有准确或密切匹配的要求。系统发育的放置本身构成了有价值的分析工具,但也需要有很多下游工具来解释其结果。一个常见用例是分析从元基因组测序获得的物种群落,例如通过分类分配,多样性定量,样本比较以及与环境变量相关的鉴定。在这篇评论中,我们概述了最初十年中开发的方法。特别是,这篇综述的目标是(i)激励系统发育放置的用法,并说明其某些用例,(ii)概述从原始序列到可出版的数字的完整工作流程,包括最佳实践,(iii)介绍最常见的工具和方法,以指出常见的位置和误解的方法,以显示他们的范围和误解(v)(v)(v)(v)(v)(v)的范围(V)帮助分析,可视化和解释系统发育放置数据。

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.

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