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ruanjue / smartdenovo

Ultra-fast de novo assembler using long noisy reads
GNU General Public License v3.0
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why is wtgbo skipped when using dmo overlapper in smartdenovo.pl? #40

Closed zhangrengang closed 4 years ago

zhangrengang commented 4 years ago

In smartdenovo.pl, wtgbo is used only in zmo overlapper mode. When using dmo overlapper in wtzmo, is it necessary to use wtgbo to rescue overlaps? I noticed that some overlaps between reads of high frequency, such as those derived from plastid, were missed.

ruanjue commented 4 years ago

gbo uses the same alignment algorithm (dynamic banded SW) with zmo. dmo uses k-mers synteny, so cannot cope with gbo.