OTU, ASV and Kraken2

Question

[Mgs3]

Hello everyone, I'm seeking clarification on the relationship between OTU, ASV, and Kraken2, which confuses me.

I understand that with the OTU approach, sequences are grouped into clusters if they have a similarity above a pre-set threshold, and these sequences are then compared to a database. On the other hand, the ASV approach does not involve clustering and uses a denoising approach.

However, I'm confused about the position of Kraken2. It is a taxonomic classification system that uses exact k-mer matches. Does this mean that it uses a different system from OTU or ASV, or does it use one of these systems and then move on to exact k-mer matches?

Any clarification would be helpful because I'm finding it difficult to understand. Thank you in advance.

[MatthewP]

You can install kraken2 and run a small dataset to help you understand.
Kranken2 doesn't use OTU, it searches/compares every read against taxonomy database (genome sequence), and assigns taxid for every read.

Answer 1

[Asaf]

OTU/ASV is used when analyzing 16S data.

Kraken2 is used for Whole Metagenome Sequencing.

OTU/ASV try to capture entities which are not necessarily represented in a database (although you can map the ASVs to a taxonomy through those databases) while kraken2 depends on a database for mapping the reads to known genomes. You can add the assembled metagenome to the reference database of course.