Table of Contents
There are links for my talks and posters.
A*PA
- A*PA (bioinformatic)
- Groot Koerkamp, Ragnar, and Pesho Ivanov. 2024. “Exact Global Alignment Using A with Chaining Seed Heuristic and Match Pruning.” Edited by Tobias Marschall. Bioinformatics 40 (3). https://doi.org/10.1093/bioinformatics/btae032.
- A*PA2 (WABI24)
- Groot Koerkamp, Ragnar. 2024. “A\textasteriskcenteredPA2: Up to 19 Faster Exact Global Alignment.” In 24th International Workshop on Algorithms in Bioinformatics (Wabi 2024), edited by Solon P. Pissis and Wing-Kin Sung, 312:17:1–17:25. Leibniz International Proceedings in Informatics (Lipics). Dagstuhl, Germany: Schloss Dagstuhl – Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.WABI.2024.17.
- Code
- github.com/RagnarGrootKoerkamp/astar-pairwise-aligner
- Slides
- slides.google.com/…
- Poster
- curiouscoding.nl/upload/astarpa-poster.pdf
PA-Bench
Mod-minimizers
- Mod-minimizer (WABI24)
- Groot Koerkamp, Ragnar, and Giulio Ermanno Pibiri. 2024. “The mod-minimizer: A Simple and Efficient Sampling Algorithm for Long k-mers.” In 24th International Workshop on Algorithms in Bioinformatics (Wabi 2024), edited by Solon P. Pissis and Wing-Kin Sung, 312:11:1–11:23. Leibniz International Proceedings in Informatics (Lipics). Dagstuhl, Germany: Schloss Dagstuhl – Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.WABI.2024.11.
- Code (C++)
- github.com/jermp/minimizers
- Code (Rust)
- github.com/RagnarGrootKoerkamp/minimizers
References
Daily, Jeff. 2016. “Parasail: Simd c Library for Global, Semi-Global, and Local Pairwise Sequence Alignments.” Bmc Bioinformatics 17 (1). https://doi.org/10.1186/s12859-016-0930-z.
Dijkstra, E. W. 1959. “A Note on Two Problems in Connexion with Graphs.” Numerische Mathematik 1 (1): 269–71. https://doi.org/10.1007/bf01386390.
Groot Koerkamp, Ragnar. 2024. “A\textasteriskcenteredPA2: Up to 19 Faster Exact Global Alignment.” In 24th International Workshop on Algorithms in Bioinformatics (Wabi 2024), edited by Solon P. Pissis and Wing-Kin Sung, 312:17:1–17:25. Leibniz International Proceedings in Informatics (Lipics). Dagstuhl, Germany: Schloss Dagstuhl – Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.WABI.2024.17.
Groot Koerkamp, Ragnar, and Pesho Ivanov. 2024. “Exact Global Alignment Using A with Chaining Seed Heuristic and Match Pruning.” Edited by Tobias Marschall. Bioinformatics 40 (3). https://doi.org/10.1093/bioinformatics/btae032.
Groot Koerkamp, Ragnar, and Giulio Ermanno Pibiri. 2024. “The mod-minimizer: A Simple and Efficient Sampling Algorithm for Long k-mers.” In 24th International Workshop on Algorithms in Bioinformatics (Wabi 2024), edited by Solon P. Pissis and Wing-Kin Sung, 312:11:1–11:23. Leibniz International Proceedings in Informatics (Lipics). Dagstuhl, Germany: Schloss Dagstuhl – Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.WABI.2024.11.
Hirschberg, D. S. 1975. “A Linear Space Algorithm for Computing Maximal Common Subsequences.” Communications of the Acm 18 (6): 341–43. https://doi.org/10.1145/360825.360861.
Ivanov, Pesho, Benjamin Bichsel, and Martin Vechev. 2022. “Fast and Optimal Sequence-to-Graph Alignment Guided by Seeds.” In Research in Computational Molecular Biology, 306–25. Springer International Publishing. https://doi.org/10.1007/978-3-031-04749-7_22.
Li, Heng. 2018. “Minimap2: Pairwise Alignment for Nucleotide Sequences.” Edited by Inanc Birol. Bioinformatics 34 (18): 3094–3100. https://doi.org/10.1093/bioinformatics/bty191.
Liu, Daniel, and Martin Steinegger. 2023. “Block Aligner: an adaptive SIMD-accelerated aligner for sequences and position-specific scoring matrices.” Bioinformatics, btad487. https://doi.org/10.1093/bioinformatics/btad487.
Marco-Sola, Santiago, Jordan M Eizenga, Andrea Guarracino, Benedict Paten, Erik Garrison, and Miquel Moreto. 2023. “Optimal Gap-Affine Alignment in O(s) Space.” Edited by Pier Luigi Martelli. Bioinformatics 39 (2). https://doi.org/10.1093/bioinformatics/btad074.
Marco-Sola, Santiago, Juan Carlos Moure, Miquel Moreto, and Antonio Espinosa. 2020. “Fast gap-affine pairwise alignment using the wavefront algorithm.” Bioinformatics 37 (4): 456–63. https://doi.org/10.1093/bioinformatics/btaa777.
Myers, Gene. 1986. “An $O(ND)$ Difference Algorithm and Its Variations.” Algorithmica 1 (1–4): 251–66. https://doi.org/10.1007/bf01840446.
———. 1999. “A Fast Bit-Vector Algorithm for Approximate String Matching Based on Dynamic Programming.” Journal of the Acm 46 (3): 395–415. https://doi.org/10.1145/316542.316550.
Suzuki, Hajime, and Masahiro Kasahara. 2018. “Introducing Difference Recurrence Relations for Faster Semi-Global Alignment of Long Sequences.” BMC Bioinformatics 19 (S1). https://doi.org/10.1186/s12859-018-2014-8.
Ukkonen, Esko. 1985. “Algorithms for Approximate String Matching.” Information and Control 64 (1–3): 100–118. https://doi.org/10.1016/s0019-9958(85)80046-2.
Šošić, Martin, and Mile Šikić. 2017. “Edlib: A c/c++ Library for Fast, Exact Sequence Alignment Using Edit Distance.” Edited by John Hancock. Bioinformatics 33 (9): 1394–95. https://doi.org/10.1093/bioinformatics/btw753.