Taxonomic Annotations

Now we’ve assembled and polished our metagenome, it’s time to start using it! In this lesson we will find out which species are present in our sample using taxonomic assignment. This is possible due to the vast amount of sequence data that already exists. We can compare our reads to a database of these sequences and see where the best matches are.

There are a few ways of doing this but we will be using a strategy called k-mers for high accuracy and rapid classification. We’ll then go on to visualise our classification results using an interactive browser application.

After looking at our taxonomy we will use our results to explore and visualise the diversity of our sample.

By the end of this lesson you will be able to:

apply Kraken2 to perform taxonomic assignment using exact k-mer matches
use Pavian to visualise and compare samples dynamically
understand α and β diversity
calculate a biological observation matrix (BIOM) from Kraken output using KrakenBiom
plot metagenome diversity using the phyloseq library

Schedule

00:00	1. Taxonomic Assignment	How can I assign a taxonomy to my raw reads? How can I visualise these assignments?
00:45	2. Diversity Tackled With R	What are α and β diversity? What are the metrics used to measure these? How can I obtain the abundance of the reads? How can I use R to explore diversity?
01:35	3. Taxonomic Analysis with R	How can we use standard R methods to summarise metagenomes? How can we plot the shared and unique compositions of samples? How can we compare samples with very different numbers of reads?
02:35	Finish

The actual schedule may vary slightly depending on topics and exercises chosen by the instructor.