121 K-mers, Sourmash, and Open Source Software - More Conversations with Titus Brown
Update: 2024-02-01
Description
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/
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/
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