I write about pairwise alignment , minimizers , and HPC/high throughput bioinformatics software.
See projects for background and links, and posts for all posts.
Highlighted posts
- September 2024 Practical minimizers
- July 2024 Computing random minimizers, fast
- June 2024 A near-tight lower bound on minimizer density
- March 2024 A*PA2: Up to 19x faster exact global alignment
- January 2024 Mod-minimizers and other minimizers
- January 2024 One Billion Row Challenge
- December 2023 Perfect NtHash for Robust Minimizers
- September 2023 PTRHash: Notes on adapting PTHash in Rust
- November 2022 String algorithm visualizations
- April 2022 A survey of exact global pairwise alignment
- May 2021 28000x speedup with Numba.CUDA