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 MinHashHow Sourmash handles k-mers for metagenomic comparisons vs. MASHThe modhash and bottom sketch approaches used in SourmashDealing with sequencing errors and noise in k-mer dataSourmash as a reference-based method, and applications for metagenomicsTitus' focus on building reusable libraries and APIs vs one-off toolsRecruiting collaborators through "nerd sniping" with interesting problemsThe open source philosophy that motivates Titus' software workOverall, 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/s13059-020-02066-4Sourmash - https://www.biorxiv.org/content/10.1101/2022.01.11.475838v2IBD exploration - https://dib-lab.github.io/2021-paper-ibd/