120 Scaling Metagenomic Search with Sourmash - Conversations with Titus Brown
MP3•Epizód kép
Manage episode 396029808 series 3381906
A tartalmat a Micro Binfie Podcast and Microbial Bioinformatics biztosítja. Az összes podcast-tartalmat, beleértve az epizódokat, grafikákat és podcast-leírásokat, közvetlenül a Micro Binfie Podcast and Microbial Bioinformatics vagy a podcast platform partnere tölti fel és biztosítja. Ha úgy gondolja, hogy valaki az Ön engedélye nélkül használja fel a szerzői joggal védett művét, kövesse az itt leírt folyamatot https://hu.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/
…
continue reading
128 epizódok