About the question for polishing long reads

[MissLiXin]

I found that I can correct genome using long reads through nextpolish2.py in the lib directory of NextPolish after mapping and indexing, but we also can correct genome using long reads through seting parameters in the [lgs_option] in the config file (run.cfg), so I wanna know what's the difference between these two ways?

[moold]

No difference, please see the Optional part at QUICK RUN section in the main page. The first strategy is to do the alignment by yourself, another is to use the NextPolish pipeline to do the alignment.