Released on February 1, 2024
Back to episode listIn this episode, Andrew Page and Lee Katz continue their conversation with Titus Brown, delving deeper into his work with k-mers, Sourmash, and open source software development.
K-mers for Analyzing Sequencing Data: The discussion focuses on how k-mers are used in sequencing data analysis and how Sourmash builds on the MinHash technique.
Metagenomic Comparisons: A comparison between how Sourmash and MASH handle k-mers for metagenomic data.
Technical Approaches: Explanation of the modhash and bottom sketch methods used in Sourmash to improve data handling.
Noise and Error Management: Addressing how sequencing errors and noise in k-mer data are dealt with in Sourmash.
Sourmash as a Reference-Based Method: Exploring the applications of Sourmash in metagenomics and how it functions as a reference-based method.
Reusable Libraries and APIs: Titus discusses his focus on building reusable libraries and application programming interfaces, as opposed to creating single-use tools.
Collaborator Recruitment: The concept of "nerd sniping" with intriguing problems to recruit new collaborators.
Open Source Philosophy: Insight into the open source philosophy that motivates Titus in his software work.
Overall, the conversation provides insight into Titus' approach to bioinformatics software, emphasizing quick iteration, usability, and open source development.