Proceedings of the Workshop on Computation: Theory and Practice (WCTP 2025)

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Bi-WaveX: a SIMD AVX-512 implementation of the Bi-directional Wavefront Alignment Algorithm

Authors
Dane Marcus Chan1, *, Christian Mir Castillo1, Raphael Jeremiah Tan Ai1, Roger Luis Uy1
1De La Salle University, 2401 Taft Avenue, Manila, Philippines
*Corresponding author. Email: dane_chan@dlsu.edu.ph
Corresponding Author
Dane Marcus Chan
Available Online 30 April 2026.
DOI
10.2991/978-94-6239-638-8_23How to use a DOI?
Keywords
read-mapping; alignment; wavefront; bi-directional wavefront; alignment algorithm; single instruction multiple data
Abstract

Sequence alignment is the process of aligning two genomic sequences. It is the first step in various bioinformatics processes and is essential in many fields of genomics and bionformatics, such as de novo genome assembly and variant detection. One such sequence alignment algorithm is the Bi-Directional Wavefront Alignment (BiWFA) algorithm, which guarantees optimal alignment with O(ns) time and O(s) space complexity. In this paper, a novel approach is presented wherein AVX-512 Single Instruction Multiple Data (SIMD) instructions are integrated into the BiWFA algorithm. Its execution time is then measured and compared against the original BiWFA library, wherein it exhibited speedups of up to 4.67x from the original.

Copyright
© 2026 The Author(s)
Open Access
Open Access This chapter is licensed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International License (http://creativecommons.org/licenses/by-nc/4.0/), which permits any noncommercial use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license and indicate if changes were made.

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Volume Title
Proceedings of the Workshop on Computation: Theory and Practice (WCTP 2025)
Series
Atlantis Highlights in Computer Sciences
Publication Date
30 April 2026
ISBN
978-94-6239-638-8
ISSN
2589-4900
DOI
10.2991/978-94-6239-638-8_23How to use a DOI?
Copyright
© 2026 The Author(s)
Open Access
Open Access This chapter is licensed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International License (http://creativecommons.org/licenses/by-nc/4.0/), which permits any noncommercial use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license and indicate if changes were made.

Cite this article

risenwbib
TY  - CONF
AU  - Dane Marcus Chan
AU  - Christian Mir Castillo
AU  - Raphael Jeremiah Tan Ai
AU  - Roger Luis Uy
PY  - 2026
DA  - 2026/04/30
TI  - Bi-WaveX: a SIMD AVX-512 implementation of the Bi-directional Wavefront Alignment Algorithm
BT  - Proceedings of the  Workshop on Computation: Theory and Practice (WCTP 2025)
PB  - Atlantis Press
SP  - 466
EP  - 480
SN  - 2589-4900
UR  - https://doi.org/10.2991/978-94-6239-638-8_23
DO  - 10.2991/978-94-6239-638-8_23
ID  - Chan2026
ER  -