Ragnar Groot Koerkamp

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 selection and sampling schemes
  ideas minimizers highlight
• July 2024 Computing random minimizers, fast
  results walkthrough highlight hpc minimizers nthash
• June 2024 A near-tight lower bound on minimizer density
  results highlight minimizers math
• March 2024 A*PA2: Up to 19x faster exact global alignment
  paper highlight pairwise-alignment astar hpc
• January 2024 Mod-minimizers and other minimizers
  ideas survey lablog highlight minimizers
• January 2024 One Billion Row Challenge
  lablog highlight hpc
• December 2023 Perfect NtHash for Robust Minimizers
  results highlight nthash math
• September 2023 PTRHash: Notes on adapting PTHash in Rust
  results lablog highlight mphf hpc
• November 2022 String algorithm visualizations
  ideas highlight suffix-array visualization
• April 2022 A survey of exact global pairwise alignment
  survey highlight pairwise-alignment
• May 2021 28000x speedup with Numba.CUDA
  results walkthrough highlight hpc