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How can we be certain that they aren't keeping a copy of our genome and/or sending it to other people?

Speaking of this issue, is there no FLOSS effort to create software that could provide this analyzing service?

Almost all the software used in biology is FLOSS. The problem is you need a lab process to get the data in the first place.

Say I have my genome in a text file, is there actually software that could give me disease predisposition data?