BG7 is a bacterial genome annotation system, designed from the start with NGS data in mind. If you want to know more about BG7: http://bg7.ohnosequences.com
There is a jars folder where the last version of each program can be found; Source code can be found (somewhat unexpectedly) under the src folder.
Most documentation is at the companion wiki, bg7/bg7/wiki
BG7 is licensed under the Affero General Public License version 3: AGPLv3