TODO: Make tool compatible with metadata or mixed reads datasets

[kbessonov1984]

Currently version 1.0.0 of the tool only allows to type single culture/pure E.coli inputs. Since often biological inputs are contaminated, mixed culture or of metadata type, there is a growing need to add read binning capability to the tool.
This feature is non-trivial especially for closely related E.coli species
Need to

• explore existing solutions
• test feasibility