Ragnar Groot Koerkamp

PhD Computational Biology @ BMI ETH Zurich

Publications

Full list here.

May 2024
The mod-minimizer: a simple and efficient sampling algorithm for long k-mers

Ragnar Groot Koerkamp and Giulio Ermanno Pibiri bioRxiv

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
Mod-minimizers
A minimizer scheme with optimal density for large k, with Giulio Ermanno Pibiri

Posts

Summaries and ideas on various topics.

Notes

Thoughts and ideas mostly written down for myself for future reference.