120 Scaling Metagenomic Search with Sourmash - Conversations with Titus Brown
Update: 2024-01-18
Description
In this final episode with Titus Brown, the conversation focuses on his work scaling metagenomic search with Sourmash:
An overview of what Sourmash does - sketching and comparing large k-mer datasets
How the sampling approach enables analyses like containment estimation
Exciting capabilities of the Branchwater tool for multi-threaded real-time SRA search
Scaling to search across millions of metagenomes in seconds with WebAssembly
Potential public health applications for tracking and sourcing pathogens
Important caveats around resolution limits and need for follow-up analyses
Ongoing work to characterize the technique's specificity and sensitivity
Overall, this episode highlights the massive scaling Sourmash enables for metagenomic search, and the potential use cases in public health, while acknowledging current limitations and uncertainties. Titus emphasizes the need to precisely convey what bioinformatic tools can and cannot do as research continues.
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/
An overview of what Sourmash does - sketching and comparing large k-mer datasets
How the sampling approach enables analyses like containment estimation
Exciting capabilities of the Branchwater tool for multi-threaded real-time SRA search
Scaling to search across millions of metagenomes in seconds with WebAssembly
Potential public health applications for tracking and sourcing pathogens
Important caveats around resolution limits and need for follow-up analyses
Ongoing work to characterize the technique's specificity and sensitivity
Overall, this episode highlights the massive scaling Sourmash enables for metagenomic search, and the potential use cases in public health, while acknowledging current limitations and uncertainties. Titus emphasizes the need to precisely convey what bioinformatic tools can and cannot do as research continues.
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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