Augmented Thresholds for MONI

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 l...

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Published in:arXiv.org 2022-11
Main Authors: Martínez-Guardiola, César, Brown, Nathaniel K, Silva-Coira, Fernando, Köppl, Dominik, Gagie, Travis, Ladra, Susana
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creator Martínez-Guardiola, César
Brown, Nathaniel K
Silva-Coira, Fernando
Köppl, Dominik
Gagie, Travis
Ladra, Susana
description 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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title Augmented Thresholds for MONI
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