5 papers
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…
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…
Merging RLBWTs adaptively
Travis Gagie
We show how to merge two run-length compressed Burrows-Wheeler Transforms (RLBWTs) into a run-length compressed extended Burrows-Wheeler Transform (eBWT) in space and $O ((…
r*-indexing
Travis Gagie
Let be a text over an alphabet of size , let be the sum of the numbers of runs in the Burrows-Wheeler Transforms of and its reverse…
Tag arrays
Travis Gagie
The Burrows-Wheeler Transform (BWT) moves characters with similar contexts in a text together, where a character's context consists of the characters immediately following it. We s…