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120 Scaling Metagenomic Search with Sourmash - Conversations with Titus Brown
Manage episode 396029808 series 3381906
Innehåll tillhandahållet av Micro Binfie Podcast and Microbial Bioinformatics. Allt poddinnehåll inklusive avsnitt, grafik och podcastbeskrivningar laddas upp och tillhandahålls direkt av Micro Binfie Podcast and Microbial Bioinformatics eller deras podcastplattformspartner. Om du tror att någon använder ditt upphovsrättsskyddade verk utan din tillåtelse kan du följa processen som beskrivs här https://sv.player.fm/legal.
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/
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