I saw Java and SQLite, but what ones are made in pure java and are platform independent? Also which would be the best to start with? I have never used sqlite but I assume it is
SQLite is getting quite a lot of hype in other language domains, however with Java you have something else available:
As for tools, well, that varies a lot. Most of the Hypersonic family products for example are mainly meant for unit testing which means that you can unit test your DB Schemas and actual queries quite easily with (almost) plain Java code.