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 databasesSourmash as a versatile search tool, not a curated databaseThe need for high confidence in taxonomic assignment in public healthMost microbial assignment tools have low specificity or sensitivityPossible ways to achieve perfect species classification (in theory)The challenges around defining species based on small genomic differencesInteresting cryptography concept of 'unicity' distance for classificationConveying the nuances and uncertainties in taxonomic assignmentThe 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/s13059-020-02066-4Sourmash - https://www.biorxiv.org/content/10.1101/2022.01.11.475838v2IBD exploration - https://dib-lab.github.io/2021-paper-ibd/