Ragnar {Groot Koerkamp}

Postdoc High Throughput Bioinformatics @ KIT Karlsruhe

I write about bioinformatics: pairwise alignment, minimizers, HPC, data structures (text-indexing, perfect hashing), and some devops. You might also be interested in my surveys and lablogs. Be warned that some posts are quick/unfinished notes.

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

Recent

March 2026 NordVPN refund dark patterns
misc
March 2026 Route Planning using Customizable Contraction Hierarchies
lablog data-structure route-planning hpc
February 2026 Wheeler graphs
survey data-structure text-indexing highlight
February 2026 DEFLATE, gzip, zlib, libz, et al.
devops linux highlight
January 2026 QuadRank: Engineering a High Throughput Rank
paper hpc data-structure
January 2026 Recent results on hash tables
survey data-structure
January 2026 Releasing Rust SIMD binaries to GitHub, BioConda, and PyPI
devops rust simd software highlight
January 2026 Trying to understand DDR memory
lablog devops hpc linux highlight
January 2026 Quotes from "The Evolution of Mathematical Software"
paper-review quote hpc data-movement

Thesis chapters

April 2025 Thesis: Optimal Throughput Bioinformatics
thesis
April 2025 A History of Pairwise Alignment
thesis survey pairwise-alignment
April 2025 Low Density Minimizers
thesis survey minimizers
April 2025 Beyond Global Alignment
thesis pairwise-alignment
April 2025 High Throughput Bioinformatics
thesis hpc

Papers

January 2026 QuadRank: Engineering a High Throughput Rank
paper hpc data-structure
August 2025 QuickHeap: the fastest priority queue
paper hpc data-structure software
February 2025 PtrHash: Minimal Perfect Hashing at RAM Throughput
paper mphf data-structure software
July 2024 SimdMinimizers: Computing random minimizers, fast
paper walkthrough hpc minimizers nthash software
June 2024 A near-tight lower bound on minimizer density
paper minimizers math
March 2024 A*PA2: Up to 19x faster exact global alignment
paper pairwise-alignment astar hpc software

Featured

February 2026 Wheeler graphs
survey data-structure text-indexing highlight
February 2026 DEFLATE, gzip, zlib, libz, et al.
devops linux highlight
January 2026 Releasing Rust SIMD binaries to GitHub, BioConda, and PyPI
devops rust simd software highlight
January 2026 Trying to understand DDR memory
lablog devops hpc linux highlight
December 2025 Asymptotic elevators
misc physics highlight
December 2025 Overview of static data structures
survey data-structure mphf highlight
November 2025 Distributing Rust SIMD Binaries
devops highlight
August 2025 Three log scientist
proposition highlight
March 2025 SimdSketch: a fast bucket sketch
results survey sketching hpc software highlight
February 2025 Thoughts on Consensus MPHF and tiny pointers
paper-review mphf data-structure highlight
June 2024 CPU performance
highlight hpc wip
September 2023 PtrHash: Notes on adapting PTHash in Rust
lablog mphf hpc highlight
August 2023 Bitpacking and approximate string matching
survey pairwise-alignment bitpacking wip highlight
November 2022 String algorithm visualizations
ideas highlight text-indexing visualization data-structure
September 2022 Revised Oxford Bioinformatics latex template
devops highlight
April 2022 Benchmark attention points
devops note hpc highlight
May 2021 28000x speedup with Numba.CUDA
results walkthrough highlight hpc

All posts