JabRef is a powerful open source bibliography/reference manager GUI program that has tools for merging bib-files, or for importing one file into another via
File --> Import into current database/library. JabRef works with the standard LaTeX bibliography format BibTeX, and has some duplicate search and other resolving capabilities such as Find duplicates, Merge entries, Check integrity and Cleanup/Delete/Import entries, and so on, which can be accessed via the menu. One can select "Deselect all duplicates" through
File --> Import/Append into current/new database/library or export all/selected entries. This functionality checks for duplicates and all duplicates can be deselected easily by using "Deselect all Duplicates" or similar button depending on the JabRef version. It also offers capability to merge two databases and thus obtain a set of unique references, with the entries in the resulting new database arranged alphabetically, by just selecting "Deselect all duplicates" before merging the two databases. Check
Merge two BibTeX files and
Cleaning up a .bib file for other tools that can be used to merge, clean or rearrange entries in the bib-files databases. The new version of JabRef can actually do a lot more.
Install JabRef via snap
To install JabRef on Ubuntu versions between 14.04 LTS (Trusty Tahr) and 15.10 (Wily Werewolf), and for Ubuntu flavours that don’t include snap by default, snap can be installed from the Ubuntu Software Centre by searching for snapd, or alternatively install snapd from the command line:
sudo apt-get update
sudo apt-get install snapd
If you are running Ubuntu 16.04 LTS (Xenial Xerus) or later version, including Ubuntu 18.04 LTS (Bionic Beaver), Ubuntu 18.10 (Cosmic Cuttlefish) and Ubuntu 19.04 (Disco Dingo), snap is already installed, and thus you can install JabRef by executing the command:
sudo snap install jabref --beta
Eli