Goby can be used either as a set of predefined utilities (see current operation modes), or as a software framework to develop new NGS data analysis pipelines. In the first case, it is likely that you will script pipelines that use one Goby mode after another. In some cases, you will find that it is simpler to write a new utility with the Goby API.
Goby is written in the Java programming language and portions of the core framework have been ported to C++ and Python. We provide extensive documentation for the Goby Java API in the JavaDoc format and the Goby Python API in Epydoc format. The section called Developing with Goby offers code snippets that demonstrate how to program the most common tasks that Goby supports. In addition, please consult the source distribution and the source of the JUnit tests distributed with the project. You can learn a lot about how to use Goby for your own projects by studying the way current modes are implemented.
Let us know if you have questions or what you thought about the package or documentation. We welcome any constructive comment. If you don’t like something, please let us know as well: there are good chances we can address the problem in a next release if we know about it.