This workshops introduces some core concepts and basic skills in the analysis of whole metagenome shotgun experiments.

The goal is to present:

1. What information we can extract from the gDNA sequencing of a microbial community (whole metagenome shotgun)
2. The difference between read based approaches (profiling) and de novo assembly (MAGs)
3. How to evaluate the quality of the sequencing and how to remove unwanted reads (QC, host removal,…)

What we will learn to do

In terms of tools we will:

1. Remove host reads using Hostile (and other methods)
2. Perform a taxonomic profiling (who is there?) of the prokaryome using MetaPhlAn 4 and the overall profiling using Kraken2, comparing the advantages and disadvantages of each tool
3. Perform a functional profiling (what are they doing?) using HUMAnN
4. Assemble the reads with MegaHit, to produce a set of contigs. We will see what a co-assembly is and when it’s useful to do it
5. See how to perform the backmapping (sometimes called read recruitment), and what information we can extract from the coverage tracks, using CoverM
6. Try to group contigs belonging to the same genome (Binning), using SemiBin2
7. Evaluate the completeness and contamination of bins (CheckM2, BUSCO), and see how to dereplicate them with dRep, and how to assign a taxonomy using GTDBtk
8. Finally, we will see how to perform manual binning and explore metagenomics assemblies using Anvi’o

---