Background Structural variants (SVs) and metagenomics remain challenging areas in genomics, requiring new tools and collaborative solutions. Hackathons provide a rapid, team-based approach to prototyping and innovation. Methods In August 2024, 48 scientists from six continents convened at Baylor College of Medicine for the Sixth Structural Variant Codeathon. Participants worked in interdisciplinary teams over three days, using public datasets and cloud-based infrastructure to design and implement computational tools. Results Eight projects were developed, addressing topics such as tandem repeat annotation, structural variant discovery, benchmarking, pangenome visualization, and machine learning applications. Each project produced open-source software, with repositories openly available on GitHub and archived on Zenodo. Conclusions The hackathon fostered global collaboration and generated reproducible, community-driven tools. These outputs provide new resources for structural variation and metagenomics research and demonstrate the effectiveness of hackathons in advancing genomic science.