I think that it would be better if SSHash were used as a submodule, to better highlight the "separation of concerns".
The only current modifications are done in the streaming query object, but that can also be reflected in the SSHash repo.
Or, are there any hard limits to this?

For the moment, we can leave everything as it is, of course.
But in the long term, I think piscem should highlight the composition SSHash+contig-table.