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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.

http://www.sagemath.org/doc/reference/sage/graphs/graph_generators.html#sage.graphs.graph_generators.GraphGenerators.nauty_geng

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 :-)

Nathann