I've never used it, but I've seen people on HN recommend Attic. It dedups and encrypts. https://attic-backup.org
Personally, I use git-annex, which isn't exactly a backup tool but a general distributed file manager which can, among other things, automatically make encrypted copies of the files to various places (SSH servers, S3, Google Drive, etc).
Both do dedup and encryption, Attic can also store the data remotely via SSH (either with or without installation on the remote end) and Obnam can handle remote storage to an SFTP server.
It's an almost completely transparent user-space filesystem. Basically you store your files in a given folder, and it automatically stores a parallel encrypted copy in a different folder.