Introduces the first cache-friendly indexing strategy for Wheeler DFAs that combines binary search and sequential scans, achieving up to 500x speedup on pangenome graphs at up to 15x space cost.
A survey of sequence alignment algorithms for next-generation sequencing.Briefings Bioinform., 11(5):473–483, 2010
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Faster Cache-Efficient Pattern Matching for Deterministic Wheeler Pangenome Graphs
Introduces the first cache-friendly indexing strategy for Wheeler DFAs that combines binary search and sequential scans, achieving up to 500x speedup on pangenome graphs at up to 15x space cost.