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Hellooooooo !!

I can't answer for the graph database problem (no Sage installed on my computer), but there is a way for you to use Nauty through Sage !

If you have not installed the spkg already, you can do it by typing sage -i nauty in a console, or something like install_package("nauty") from the inside of Sage.

Afterwards you will bd able to use the nauty_geng method, with a "-c" flag that probably interests you.

Note that 11 is probably the limit of graphs that you can enumerate from within Sage, where most of the time is spent converting Nauty's graphs to Sage objects :-)