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Augmented Thresholds for MONI

Citation Author(s):
C ́esar Mart ́ınez-Guardiola, Nathaniel K. Brown, Fernando Silva-Coira, Dominik K ̈oppl, Travis Gagie, Susana Ladra
Submitted by:
Nathaniel Brown
Last updated:
2 March 2023 - 6:43am
Document Type:
Presentation Slides
Document Year:
Nathaniel K. Brown
Paper Code:

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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