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cs.DS2026
Reportable Shortcuts with RLBWTs
Travis Gagie
Backward search over a run-length compressed Burrows--Wheeler transform (RLBWT) takes one step per pattern character, even when long stretches of the pattern match material that re…
cs.DS2026
Parse indexing for discarding short pseudo-MEMs safely
Travis Gagie
Brown et al.\ (2025) described a pre-processing step, called -mer based breaking (KeBaB), that speeds up searching for long maximal exact matches (MEMs) between a pattern an…
cs.DS2026
Faster PBWT prefix-array access via batching
Travis Gagie
The positional Burrows-Wheeler Transform (PBWT) is commonly used to store haplotype panels compactly in such a way that, given a query haplotype, we can quickly find the set maxima…