RT Journal Article
T1 SeqMatcher: efficient genome sequence matching with AVX-512 extensions
A1 Espinosa, Elena
A1 Quislant-del-Barrio, Ricardo
A1 Larrosa-Jiménez, Rafael
A1 Plata-González, Óscar Guillermo
K1 Algoritmos computacionales
K1 Arquitectura de ordenadores
AB The recent emergence of long-read sequencing technologies has enabled substan-tial improvements in accuracy and reduced computational costs. Nonetheless, pair-wise sequence alignment remains a time-consuming step in common bioinformat-ics pipelines, becoming a bottleneck in de novo whole-genome assembly. Speedingup this step requires heuristics and the development of memory-frugal and efficientimplementations. A promising candidate for all of the above is Myers’ algorithm.However, the state-of-the-art implementations face scalability challenges when deal-ing with longer reads and large datasets. To address these challenges, we proposeSeqMatcher, a fast and memory-frugal genomics sequence aligner. By leveragingthe long registers of AVX-512, SeqMatcher reduces the data movement and memoryfootprint. In a comprehensive performance evaluation, SeqMatcher achieves speed-ups of up to 12.32x for the unbanded version and 26.70x for the banded versioncompared to the non-vectorized implementation, along with energy footprint reduc-tions of up to 2.59x. It also outperforms state-of-the-art implementations by factorsof up to 29.21x, 17.56x, 13.47x, 9.12x, and 8.81x compared to Edlib, WFA2-lib,SeqAn, BSAlign, and QuickEd, while improving energy consumption with reduc-tions of up to 6.78x
PB Springer Nature
YR 2024
FD 2024-12
LK https://hdl.handle.net/10630/36202
UL https://hdl.handle.net/10630/36202
LA eng
NO Espinosa, E., Quislant, R., Larrosa, R. et al. SeqMatcher: efficient genome sequence matching with AVX-512 extensions. J Supercomput 81, 355 (2025). https://doi.org/10.1007/s11227-024-06789-0
NO Funding for open access publishing: Universidad Málaga/CBUA.
DS RIUMA. Repositorio Institucional de la Universidad de Málaga
RD 20 ene 2026