In this episode, Andrew Page and Lee Katz continue their chat with Titus Brown, focusing on taxonomy assignment in metagenomics:

Topics discussed:

Dealing with contamination and low quality genomes in reference databases

Sourmash as a versatile search tool, not a curated database

The need for high confidence in taxonomic assignment in public health

Most microbial assignment tools have low specificity or sensitivity

Possible ways to achieve perfect species classification (in theory)

The challenges around defining species based on small genomic differences

Interesting cryptography concept of 'unicity' distance for classification

Conveying the nuances and uncertainties in taxonomic assignment

The conversation highlights the difficulties around taxonomic classification, especially at the species level, but explores ideas for improving accuracy. Overall it emphasizes the complexities of biology and need for transparent conveyance of uncertainties.

Papers:

Spacegraphcats - https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02066-4

Sourmash - https://www.biorxiv.org/content/10.1101/2022.01.11.475838v2

IBD exploration - https://dib-lab.github.io/2021-paper-ibd/