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cs.DS2025
KeBaB: -mer based breaking for finding long MEMs
Nathaniel K. Brown, Lore Depuydt, Mohsen Zakeri +8
Long maximal exact matches (MEMs) are used in many genomics applications such as read classification and sequence alignment. Li's ropebwt3 finds long MEMs quickly because it can of…
cs.DS2025
Suffixient Arrays: a New Efficient Suffix Array Compression Technique
Davide Cenzato, Lore Depuydt, Travis Gagie +4
The Suffix Array is a classic text index enabling on-line pattern matching queries via simple binary search. The main drawback of the Suffix Array is that it takes linear space in…
cs.DS2024
Suffixient Sets
Lore Depuydt, Travis Gagie, Ben Langmead +2
We define a suffixient set for a text to be a set of positions between 1 and such that, for any edge descending from a node to a node in the suffix tree…