6. Do it yourself

6.1. Hands-on 1: Run the metagenomic analysis on a different dataset

In this hands-on session your task is to analyse the in R the species abundance data generated by running the same dataset in a larger Kraken2 database (8Gb)

1. Download the abundance table and the associated metadata (there are more chimpanzees in this dataset).

2. Follow step-by-step section 5 and notice the differences in your output compared to the results obtained with a 2Gb database.

6.2. Hands-on 2: Run Kraken2 on an ancient dental calculus dataset

In this hands-on session your task is to analyse with the Kraken2 2Gb database samples of dental calculus from ancient humans dated to the 18th-19th century.

1. Pre-process the fastqs by removing the adapters and filtering for quality. Collapse the paired-end reads. Here is the sample sheet to run Adapter Removal in the loop [Section 2]

2. Run Kraken2 on the collapsed reads, and estimate the abundances with Bracken. [Section 3]

3. Prepare the tables for the analysis in R. [Section 4]

4. Analyse the data in R. Here is the metadata file updated with the new samples - make sure the files id in the first column correspond to your actual Bracken file names [Section 5]