121 K-mers, Sourmash, and Open Source Software - More Conversations with Titus Brown

Micro binfie podcast

In this episode, Andrew Page and Lee Katz continue their conversation with Titus Brown, diving deeper into his work on k-mers, Sourmash, and open source software development: Topics discussed: K-mers for analyzing sequencing data, and how Sourmash builds on MinHash How Sourmash handles k-mers for metagenomic comparisons vs. MASH The modhash and bottom sketch approaches used in Sourmash Dealing with sequencing errors and noise in k-mer data Sourmash as a reference-based method, and applications for metagenomics Titus' focus on building reusable libraries and APIs vs one-off tools Recruiting collaborators through "nerd sniping" with interesting problems The open source philosophy that motivates Titus' software work Overall, the conversation provides insight into Titus' approach to bioinformatics software through iterating quickly, focusing on usability, and building open source tools. 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/