119 The Challenges of Microbial Taxonomy - Conversations with Titus Brown
Update: 2024-01-04
Description
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/
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/
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