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section-ancient-metagenomics.qmd

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## [Taxonomic Profiling](taxonomic-profiling.qmd)
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One of the first questions when looking at metagenomics data is often _Who is there?_. But this question is actually not specific to (ancient) metagenomics, but in fact is a broader ecological question that has first been applied to macro ecological systems.
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In this chapter, we will show you how to answer this question at the microbial scale using methods applied to ancient metagenomics data.
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We will talk about taxonomic profiling, ecological diversity metrics, how to compare different samples and see how they relate through their community composition.
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We will learn about taxonomic profiler tools, ways to analyze and visualize taxonomic profiles, libraries to manipulate taxonomic profile tables, and libraries to compute and visualize ecological diversity metrics.
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## [_De novo_ Assembly](denovo-assembly.qmd)
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