4 papers
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…
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…
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…
Faster Maximal Exact Matches with Lazy LCP Evaluation
Adrián Goga, Lore Depuydt, Nathaniel K. Brown +3
MONI (Rossi et al., {\it JCB} 2022) is a BWT-based compressed index for computing the matching statistics and maximal exact matches (MEMs) of a pattern (usually a DNA read) with re…