Strategies for taxonomic and functional annotation of metagenomes (2nd edition)

Book chapter, 2024

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 up-to-date overview of recent software for metagenomic analysis, discussing different strategies to perform taxonomic classification, functional analysis, metagenomic assembly, and statistical comparisons between metagenomes. The most recent state-of-the-art analysis strategies are highlighted in this chapter, along with well-established robust and well-functioning software tools that still are the best for their tasks.