Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade
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 conte...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-05-01
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| Series: | Frontiers in Bioinformatics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fbinf.2022.871393/full |
| _version_ | 1817980945684234240 |
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| author | Lucas Czech Alexandros Stamatakis Alexandros Stamatakis Micah Dunthorn Pierre Barbera |
| author_facet | Lucas Czech Alexandros Stamatakis Alexandros Stamatakis Micah Dunthorn Pierre Barbera |
| author_sort | Lucas Czech |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-13T22:59:21Z |
| format | Article |
| id | doaj.art-311eab1fa1394b8f8c56c64c9a4d5ece |
| institution | Directory Open Access Journal |
| issn | 2673-7647 |
| language | English |
| last_indexed | 2024-04-13T22:59:21Z |
| publishDate | 2022-05-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Bioinformatics |
| spelling | doaj.art-311eab1fa1394b8f8c56c64c9a4d5ece2022-12-22T02:25:54ZengFrontiers Media S.A.Frontiers in Bioinformatics2673-76472022-05-01210.3389/fbinf.2022.871393871393Metagenomic Analysis Using Phylogenetic Placement—A Review of the First DecadeLucas Czech0Alexandros Stamatakis1Alexandros Stamatakis2Micah Dunthorn3Pierre Barbera4Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, United StatesComputational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, GermanyInstitute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, GermanyNatural History Museum, University of Oslo, Oslo, NorwayIndependent Researcher, Bisingen, GermanyPhylogenetic 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.https://www.frontiersin.org/articles/10.3389/fbinf.2022.871393/fullphylogenetic placementevolutionary placementphylogeneticsmetagenomicsmetabarcodingspecies diversity |
| spellingShingle | Lucas Czech Alexandros Stamatakis Alexandros Stamatakis Micah Dunthorn Pierre Barbera Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade Frontiers in Bioinformatics phylogenetic placement evolutionary placement phylogenetics metagenomics metabarcoding species diversity |
| title | Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade |
| title_full | Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade |
| title_fullStr | Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade |
| title_full_unstemmed | Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade |
| title_short | Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade |
| title_sort | metagenomic analysis using phylogenetic placement a review of the first decade |
| topic | phylogenetic placement evolutionary placement phylogenetics metagenomics metabarcoding species diversity |
| url | https://www.frontiersin.org/articles/10.3389/fbinf.2022.871393/full |
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