Examples of how to run khmer command-line scripts are included in the main khmer documentation, as well as the khmer protocols collection. However, the intrepid user may be interested in having more direct access to khmer via its Python or C++ API.
The examples/python-api and examples/c++-api directories contain several small programs that demonstrate how one would write a program that uses the khmer API.
These programs are run frequently as part of our continuous integration build, so they are quite stable.
Note, however, that unlike the khmer command-line scripts, the Python and C++ API ARE NOT under semantic versioning.
Consequently, internal changes to the khmer codebase may require changes to the API examples at any time.
We expect to have the Python API under semantic versioning by version 5.0.