Enhance polishing and downstream as hybracter

[fmalmeida]

Assess what is required and how to implement some nice features performed in https://github.com/gbouras13/hybracter such as the coupled polishing of polypolish+pypolca which seem to work nicely in a complementary manner. Maybe the plasmid assembly step. And maybe the chr reorientation step.

Check what and how can be done.