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arXiv · 2211.07794

Augmented Thresholds for MONI

César Martínez-Guardiola·Nathaniel K. Brown·Fernando Silva-Coira·Dominik Köppl·Travis Gagie·Susana Ladra
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Abstract

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.

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César Martínez-Guardiola, Nathaniel K. Brown, Fernando Silva-Coira, Dominik Köppl, Travis Gagie, Susana Ladra. 2022-11-14. Augmented Thresholds for MONI. https://arxiv.org/abs/2211.07794

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