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Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade

Czech, Lucas; Stamatakis, Alexandros ORCID iD icon 1; Dunthorn, Micah; Barbera, Pierre
1 Institut für Theoretische Informatik (ITI), Karlsruher Institut für Technologie (KIT)

Abstract:

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 10 years. In particular, the goals of this review are 1) to motivate the usage of phylogenetic placement and illustrate some of its use cases, 2) to outline the full workflow, from raw sequences to publishable figures, including best practices, 3) to introduce the most common tools and methods and their capabilities, 4) to point out common placement pitfalls and misconceptions, 5) to showcase typical placement-based analyses, and how they can help to analyze, visualize, and interpret phylogenetic placement data.


Verlagsausgabe §
DOI: 10.5445/IR/1000174224
Veröffentlicht am 16.09.2024
Originalveröffentlichung
DOI: 10.3389/fbinf.2022.871393
Scopus
Zitationen: 15
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Zitationen: 27
Cover der Publikation
Zugehörige Institution(en) am KIT Institut für Theoretische Informatik (ITI)
Publikationstyp Zeitschriftenaufsatz
Publikationsmonat/-jahr 05.2022
Sprache Englisch
Identifikator ISSN: 2673-7647
KITopen-ID: 1000174224
Erschienen in Frontiers in Bioinformatics
Verlag Frontiers Media SA
Band 2
Seiten Art.-Nr.: 871393
Vorab online veröffentlicht am 26.05.2022
Schlagwörter phylogenetic placement, evolutionary placement, phylogenetics, metagenomics, metabarcoding, species diversity, taxonomic assignment, sequence identification
Nachgewiesen in Scopus
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