Ragnar {Groot Koerkamp}

PhD High Throughput Bioinformatics @ BMI ETH Zurich

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
results walkthrough hpc binary-search popular data-structure
January 2024 One Billion Row Challenge
lablog hpc popular

Highlights

March 2025 SimdSketch: a fast bucket sketch
survey sketching highlight software
February 2025 Thesis: Optimal Throughput Bioinformatics
thesis highlight
February 2025 A History of Pairwise Alignment
thesis survey pairwise-alignment highlight
February 2025 Low Density Minimizers
thesis survey minimizers highlight
February 2025 High Throughput Bioinformatics
thesis hpc highlight
February 2025 PtrHash: Minimal Perfect Hashing at RAM Throughput
paper highlight mphf data-structure software
July 2024 SimdMinimizers: Computing random minimizers, fast
results walkthrough highlight hpc minimizers nthash software
June 2024 CPU performance
highlight hpc wip
March 2024 A*PA2: Up to 19x faster exact global alignment
paper highlight pairwise-alignment astar hpc software
November 2022 String algorithm visualizations
ideas highlight suffix-array visualization data-structure
May 2021 28000x speedup with Numba.CUDA
results walkthrough highlight hpc