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I have used two different tools: Borg, which I have used for several years. It works very well over SSH and has good configurability in all areas, from file exclusions to retention configs. It does deduplication and client side encryption.
The only reason I switched away from it was that I'm now running a Ceph cluster and wanted to back up to one of it's pools via S3. So now I'm using Restic. It has a far wider variety of backup targets, including local disk and S3. Similar to Borg, it does deduplication and does encryption.
For other OSes, I'm not really sure. I think they don't support those for their system drives but I guess it should be possible to get them to work for data drives somehow (e.g., https://github.com/maharmstone/btrfs).