[[command-line-tools]]
Command line tools
------------------

Although the full flexibility of IGoR is reachable through C\++ highlevel
functions (see the <<c,C++ section>>) we provide some command line options to
perform most frequent tasks on immune receptor sequences.

Command options are nested arguments, the general organization of the
commands follows `-arg1 --subarg1 ---subsubarg1` to reach the different
levels.

[[general]]
General
~~~~~~~

include::general_command_lines.adoc[]

include::scripts.adoc[]

