Author: Ragnar Groot Koerkamp

March 2025 [WIP] Semi-global alignment, mapping, and string searching
pairwise-alignment wip
March 2025 SimdSketch: a fast bucket sketch
survey sketching highlight
March 2025 Types of tigs
survey note
February 2025 Near-optimal sampling schemes
slides minimizers
February 2025 0. Optimal Throughput Bioinformatics
thesis highlight wip
February 2025 1. Pairwise Alignment
thesis survey pairwise-alignment highlight wip
February 2025 2. Minimizers and More
thesis survey minimizers highlight
February 2025 3. High Throughput Bioinformatics
thesis hpc highlight wip
February 2025 Minimizer papers
survey minimizers note
February 2025 [WIP] Binary search variants and the effects of batching
walkthrough binary-search wip
February 2025 Thoughts on Consensus MPHF and tiny pointers
paper-review mpfh
February 2025 PtrHash: Minimal Perfect Hashing at RAM Throughput
paper highlight mphf
January 2025 Code snippets for Latex, Rust, and Python
devops note
January 2025 Setting up traffic monitoring using GoAccess
devops linux
December 2024 Static search trees: 40x faster than binary search
results walkthrough highlight hpc binary-search
November 2024 Comments on Brisk
paper-review minimizers
November 2024 Comments on GreedyMini
paper-review minimizers
October 2024 Comments on 'When Less is More' minimizer review
paper-review minimizers
October 2024 A lemma on suffix array searching
results suffix-array
October 2024 FM-index implementations
survey
September 2024 Practical minimizers
ideas minimizers
September 2024 Calling Rust from Python
devops
September 2024 AI reading list
ai
September 2024 PACE 24
survey ilp
August 2024 [WIP] Feynman problems
wip
August 2024 Optimal throughput bioinformatics
slides
July 2024 SimdMinimizers: Computing random minimizers, fast
results walkthrough highlight hpc minimizers nthash
June 2024 A near-tight lower bound on minimizer density
results highlight minimizers math
June 2024 CPU performance
survey highlight hpc wip
June 2024 Tools for suffix array searching
survey note suffix-array binary-search
June 2024 Crates for suffix array construction
survey note suffix-array
May 2024 Thoughts on POASTA
paper-review alignment astar
March 2024 A*PA2: Up to 19x faster exact global alignment
paper highlight pairwise-alignment astar hpc
January 2024 Review of refined minimizes
paper-review
January 2024 Mod-minimizers and other minimizers
ideas survey lablog highlight minimizers
January 2024 Intro to Rust
devops rust teaching
January 2024 Notes on bidirectional anchors
method minimizers
January 2024 Notes on SsHash
method note mphf
January 2024 One Billion Row Challenge
lablog highlight hpc
December 2023 Perfect NtHash for Robust Minimizers
results nthash math minimizers
December 2023 A*PA talk @ CWI
misc pairwise-alignment teaching
December 2023 Notes on implementing Longest Common Repeat (LCR)
ideas lablog
November 2023 ALPACA/PANGAIA winter workshop notes
misc conference-notes
November 2023 Notes on writing course
misc note
October 2023 BAPCtools instruction
misc competitive-programming teaching
September 2023 PTRHash: Notes on adapting PTHash in Rust
results lablog mphf hpc
September 2023 BBHash: some ideas
method note mphf
September 2023 BitPAl bitpacking algorithm
method note pairwise-alignment bitpacking
August 2023 [WIP] Bitpacking and string searching
survey alignment wip
July 2023 Shortest paths, bucket queues, and A* on the edit graph
survey astar pairwise-alignment
July 2023 Research proposal: subquadratic string graph construction
ideas
July 2023 Loukides, Pissis, Thankachan, Zuba :: Suffix-Prefix Queries on a Dictionary
paper-review
March 2023 DSB 2023
misc conference-notes
December 2022 Doctoral plan
ideas
November 2022 One Year Of Rust
devops rust
November 2022 The complexity and performance of WFA and band doubling
survey pairwise-alignment wfa
November 2022 String algorithm visualizations
ideas highlight suffix-array visualization
November 2022 Thoughts on linear programming
ideas note
October 2022 Local Doubling
ideas pairwise-alignment
October 2022 BWT and FM-index
method suffix-array
October 2022 A Combinatorial Identity
misc note math
October 2022 Tensor embedding preserves Hamming distance
results
October 2022 Linear-time suffix array construction
method note suffix-array
September 2022 Competitive Programming Lecture
misc pairwise-alignment competitive-programming teaching
September 2022 Reducing A* memory usage using fronts
ideas note astar
September 2022 Speeding up A*: computational volumes and path-pruning
ideas pairwise-alignment astar
September 2022 Revised Oxford Bioinformatics latex template
devops
August 2022 Linear memory WFA?
ideas pairwise-alignment wfa
August 2022 Transforming match bonus into cost
ideas pairwise-alignment wfa
August 2022 Paper styleguide
misc
August 2022 Diamond optimisation for diagonal transition
ideas pairwise-alignment hpc
July 2022 Bidirectional A*
survey note astar
July 2022 The BiWFA meeting condition
ideas note pairwise-alignment wfa
June 2022 A* variants
survey astar
June 2022 IGGSY 22 Slides
misc
April 2022 Benchmark attention points
devops note hpc
April 2022 Motivation
proposition
April 2022 Variations on the WFA recursion
ideas pairwise-alignment wfa
April 2022 A survey of exact global pairwise alignment
survey pairwise-alignment
November 2021 AStarix
method note alignment astar
November 2021 Neighbour joining
method note phylogeny
October 2021 UPGMA
method note phylogeny
October 2021 RTFE
proposition
October 2021 1st law of Procrastination
proposition
October 2021 Data should be reviewed
proposition
October 2021 Hugo and ox-hugo
devops
October 2021 Hello, World!
misc
July 2021 Spaced k-mer and assembler methods
survey note genome-assembly spaced-kmers
July 2021 Ideas for assembling [long] reads
ideas genome-assembly
July 2021 Hamming Similarity Search
ideas genome-assembly
July 2021 Detached fullscreen in Sway
devops linux wayland
July 2021 Open source contributions
devops linux
July 2021 Powersearch with Vimium
devops linux
July 2021 Wayland utilities
devops linux wayland
July 2021 Browsing in the dark with Vimium and Dark Reader
devops linux
July 2021 Window switching in Sway
devops linux wayland
June 2021 Clean your homedir with XDG Base Dir
devops linux wayland
June 2021 Emacs Doom
devops linux
June 2021 Environment variables done once
devops linux wayland
May 2021 28000x speedup with Numba.CUDA
results walkthrough highlight hpc
May 2021 X1 Extreme Gen 3 - Migrating to Wayland
devops linux wayland
April 2021 SE Endurance: Early game
misc
April 2021 Hashcode 2021 Finals
misc competitive-programming
March 2021 Hashcode 2021: A lucky ride
misc competitive-programming