Fast Pangenome Matching Statistics in Compressed Space with Move Structures
Matching statistics and supermaximal exact matches (SMEMs) are key inputs for sequence homology search and classification. Methods such as MONI, PHONI, and ropebwt3 compute these statistics using compressed pangenome indexes, but are substantially slower than methods that compute approximations of matching statistics, such as pseudo-matching lengths (PMLs). PMLs can be computed quickly in a…
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