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Strategies for Taxonomic and Functional Annotation of Metagenomes

Chapter in book
Authors Johan Bengtsson-Palme
Published in Metagenomics: Perspectives, Methods, and Applications. Muniyandi Nagarajan (red.)
Pages 55–79
ISBN 9780081022689
Publisher Academic Press, Elsevier
Place of publication USA
Publication year 2018
Published at Institute of Biomedicine, Department of Infectious Medicine
Centre for antibiotic resistance research, CARe
Pages 55–79
Language en
Keywords Annotation; Annotation pipelines; Diversity; Ecosystem processes; Functional analysis; Metagenomic analysis strategies; Metagenomic assembly; Statistical methods for metagenomics; Taxonomic classification
Subject categories Bioinformatics (Computational Biology), Statistics, computer and systems science, Ecology, Microbiology


Recent advancements in DNA sequencing capacity have resulted in a flood of metagenomic data being generated, together with a myriad of computational tools for metagenomic analysis. Selecting the right tools in this jungle of options can be hard, particularly as new developments are presented almost daily. This chapter provides an overview of recent software for metagenomic analysis, discussing different strategies to perform taxonomic classification, functional analysis, metagenomic assembly, and statistical comparisons between metagenomes. The chapter also considers the use of automated computational “pipelines” for analysis of metagenomic data and highlights their pros and cons in comparison to running the analyses one by one. Currently, it is hard to point out any tools that obviously perform better in every situation, but there are certain analysis strategies that clearly should be avoided. Those are highlighted in this chapter, and instead robust and well-functioning software tools that can be used are suggested.

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