There's a 10-year-old question 10-year-old question about using nauty to get canonical graphs. I take it this is still not implemented.
On the other hand, the documentation says that canonical_label() has parameter algorithm which can take value 'bliss', but I can't seem to get it work. I'm on Debian stable using sagemath as a Debian package (version 9.2), and also bliss and libblis2 are installed. The error is simply
ModuleNotFoundError: No module named 'sage.graphs.bliss'
I feel like it's a simply matter of letting sagemath know that bliss is out there.