This tutorial will guide you through the process of analyzing metagenomic data using QIIME 2 framework and MOSHPIT. The tutorial is divided into several chapters, each focusing on a different aspect of metagenomic data analysis. We will use a small published dataset to demonstrate the capabilities of most of the methods available in MOSHPIT.
We will begin by setting up our computational environment and fetching all the necessary data (see Setup and Data retrieval). Then, we will move to quality control and filtering of the raw reads (see Quality control). Once we have our clean dataset, we can start by recovering metagenome-assembled genomes (MAGs) (see here), followed by taxonomic classification of reads and MAGs themselves (see Taxonomic classification). Finally, we will estimate perform functional annotation of the dereplicated MAGs (see Functional annotation).
Let’s dive in!