Chapter 8 Taxonomic profiling

There are a number of methods for determining the species composition of a metagenomic dataset, but for the purposes of this practical we will use Kraken2 & Bracken (Bayesian Reestimation of Abundance with KrakEN). Kraken2 classifies short DNA with taxonomic labels and is frequently used for metagenomic studies. Bracken uses the taxonomic labels assigned by Kraken2 to compute the abundance of species in a set of DNA sequences.

First, we'll make a new directory for it and move into it, after returning home:

cd ..
mkdir 3-Taxonomy
cd 3-Taxonomy