Metagenomics and Kraken (#7)
July 9, 2017
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.
- 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)
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.
Subscribe to the bioinformatics chat on Apple Podcasts, Pocket Casts, Spotify, or any other podcasting app via the RSS feed link. You can also follow the podcast on Mastodon and Twitter and support it on Patreon.