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Augmented Thresholds for MONI
- Citation Author(s):
- Submitted by:
- Nathaniel Brown
- Last updated:
- 2 March 2023 - 6:43am
- Document Type:
- Presentation Slides
- Document Year:
- 2023
- Event:
- Presenters:
- Nathaniel K. Brown
- Paper Code:
- 253
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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.