Publications
Full list here.
- March 2024
- A*PA2: Up to 20 times faster exact global alignment.
Ragnar Groot Koerkamp, bioRxiv
- Jan 2024
- Exact global alignment using A* with seed heuristic and match
pruning.
Ragnar Groot Koerkamp and Pesho Ivanov, Bioinformatics, bioRxiv
Projects
More projects, ideas, and todos are here.
- A*PA, A*PA2
- Fast pairwise alignment, with Pesho Ivanov
- PA-Bench
- Benchmarking pairwise aligners, with Daniel Liu
- PTRHash
- Fast and small minimal perfect hash function
- Minimizers
- Find a tight lower bound on minimizer density. With Giulio Ermanno Pibiri
Posts
Summaries and ideas on various topics.
- March 2024 A*PA2: Up to 20x faster exact global alignment
- January 2024 Minimizers and variations
- January 2024 Notes on bidirectional anchors
- January 2024 One Billion Row Challenge
- December 2023 Perfect NtHash for Robust Minimizers
- September 2023 PTRHash: Notes on adapting PTHash in Rust
- July 2023 Research proposal: subquadratic string graph construction
- November 2022 The complexity and performance of WFA and band doubling
- November 2022 String algorithm visualizations
- October 2022 Local Doubling
- September 2022 Speeding up A*: computational volumes and path-pruning
- August 2022 Linear memory WFA?
- August 2022 Transforming match bonus into cost
- August 2022 Diamond optimisation for diagonal transition
- April 2022 Variations on the WFA recursion
- April 2022 Glossary
- April 2022 A review of exact global pairwise alignment
- October 2021 Spaced K-mer Seeded Distance
- October 2021 Open Science
- July 2021 Ideas for assembling [long] reads
- July 2021 Hamming Similarity Search
- May 2021 28000x speedup with Numba.CUDA
Notes
Thoughts and ideas mostly written down for myself for future reference.
- January 2024 Review of refined minimizes
- January 2024 Intro to Rust
- December 2023 A*PA talk @ CWI
- December 2023 Notes on implementing Longest Common Repeat (LCR)
- November 2023 ALPACA/PANGAIA winter workshop notes
- November 2023 Notes on writing course
- October 2023 [WIP] PTRhash: Improving the PTHash Minimal Perfect Hash Function
- October 2023 BAPCtools instruction
- September 2023 BBHash: some ideas
- September 2023 BitPAl bitpacking algorithm
- August 2023 [WIP] Bitpacking and string searching
- July 2023 Shortest paths, bucket queues, and A* on the edit graph
- July 2023 Loukides, Pissis, Thankachan, Zuba :: Suffix-Prefix Queries on a Dictionary
- March 2023 DSB 2023
- December 2022 Doctoral plan
- November 2022 One Year Of Rust
- November 2022 Thoughts on linear programming
- October 2022 Links and references for A*PA & A*PA2 poster
- October 2022 BWT and FM-index
- October 2022 A Combinatorial Identity
- October 2022 Tensor embedding preserves Hamming distance
- October 2022 Linear-time suffix array construction
- September 2022 Competitive Programming Lecture
- September 2022 Reducing A* memory usage using fronts
- September 2022 Revised Oxford Bioinformatics latex template
- August 2022 Paper styleguide
- July 2022 Bidirectional A*
- July 2022 The BiWFA meeting condition
- June 2022 A* variants
- June 2022 IGGSY 22 Slides
- April 2022 Benchmark attention points
- April 2022 Motivation
- April 2022 Proof sketch for linear time seed heuristic alignment
- December 2021 Pruning for A* heuristics
- November 2021 AStarix
- November 2021 Neighbor joining
- October 2021 UPGMA
- October 2021 RTFE
- October 2021 1st law of Procrastination
- October 2021 Data should be reviewed
- October 2021 Hugo and ox-hugo
- October 2021 Hello, World!
- July 2021 Spaced k-mer and assembler methods