Genome-scale algorithmics (GSA)
MUMs
Maximal Unique Matches (MUMs) computed with a bidirectional BWT-index. This is an implementation of one of the results in our ESA 2013 paper, plugged into to Simon Gog's SDSL library. We conducted a small benchmark to show it is competive. Two versions of human chromosome 20 (2*60 MB) were used as input, and running time and peak space usage was compared againts vmatch and mummer. We used suffix array sampling frequency 256 in our implementation; the mechanism described in ESA paper to avoid suffix array samples completely was not implemented.
time (s) | space (MB) | |
ours | 751 | 207 |
vmatch | 437 | 938 |
mummer | 97 | 930 |