yubikey-manager is a Python application requiring some dependencies for it to be installed from the Python repositories, because it is not yet in the official Debian package repository. Here is how:
apt-get install swig libpcsclite-dev
pip3 install yubikey-manager --user
Here is the main commandline utility:
~/.local/bin/ykman
pcscd and libpcsclite-dev is needed too.
Else you might get: smartcard.pcsc.PCSCExceptions.EstablishContextException: ‘Failure to establish context: Service not available.’