I write about pairwise alignment , minimizers , and HPC/high throughput bioinformatics software.
See projects for background and links, and posts for all posts.
Popular
- December 2024 Static search trees: 40x faster than binary search
- January 2024 One Billion Row Challenge
Highlights
- March 2025 SimdSketch: a fast bucket sketch
- February 2025 Thesis: Optimal Throughput Bioinformatics
- February 2025 A History of Pairwise Alignment
- February 2025 Low Density Minimizers
- February 2025 High Throughput Bioinformatics
- February 2025 PtrHash: Minimal Perfect Hashing at RAM Throughput
- July 2024 SimdMinimizers: Computing random minimizers, fast
- June 2024 CPU performance
- March 2024 A*PA2: Up to 19x faster exact global alignment
- November 2022 String algorithm visualizations
- May 2021 28000x speedup with Numba.CUDA