Taxonomic profiling

There are a number of methods for determining the species composition of a metagenomic dataset. For the purposes of this practical, we will use Kraken2 and Bracken (Bayesian Reestimation of Abundance with KrakEN).

Kraken2 classifies short DNA sequences by assigning taxonomic labels and is widely used in metagenomic studies. Bracken builds on the output of Kraken2 to estimate the relative abundance of taxa in a sample.

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1 Directory setup

First, return to your home directory, create a new directory for taxonomic profiling, and move into it.

cd 
mkdir 3-Taxonomy
cd 3-Taxonomy

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