the bioinformatics chat

What is metagenomics and how is it different from phylotyping?

What is Kraken and how can it be faster than BLAST?

Let’s try to sort this out.

Sections:

• Culturing and its limitation (00:18)
• Metagenomics vs phylotyping (1:43)
• BLAST (5:53)
• The idea behind Kraken (8:14)
• How Kraken organizes its database (18:08)

Links:

• The paper about Kraken
• A freely accessible (though a bit dated) book on metagenomics

Correction: in this episode, I incorrectly state that Kraken operates on phylogenetic trees, whereas in fact it operates on taxonomic trees.

In practice this means that when Kraken cannot decide among several species, it assigns the read to their lowest common taxon (genus, family etc.), not their latest common evolutionary ancestor.

If you enjoyed this episode, please consider supporting the podcast on Patreon.