YubiKey Manager (ykman) is a command line tool for configuring a YubiKey over all transports. It is capable of reading out device information as well as configuring several aspects of a YubiKey, including enabling or disabling connection transports and programming various types of credentials.
YubiKey is a specific series of personal Hardware Security Modules, meant to protect private keys tied to its users (for 2nd factor authentication, use with OpenPGP, ...).