MONI (Rossi et al., 2022) can store a pangenomic dataset T in small space and later, given a pattern P, quickly find the maximal exact matches (MEMs) of P with respect to T. In this paper we consider its one-pass version (Boucher et al., 2021), whose query times are dominated in our experiments by longest common extension (LCE) queries. We show how a small modification lets us avoid most of these queries and thus significantly speeds up MONI in practice while only slightly increasing its size.
Cite
@article{arxiv.2211.07794,
title = {Augmented Thresholds for MONI},
author = {César Martínez-Guardiola and Nathaniel K. Brown and Fernando Silva-Coira and Dominik Köppl and Travis Gagie and Susana Ladra},
journal= {arXiv preprint arXiv:2211.07794},
year = {2022}
}