Welcome to the documentation of the SeqAn library. This web-site contains the API reference (documentation of our interfaces) and more elaborate Tutorials and How-Tos.

If you are new to SeqAn, we recommend that you begin by reading Quick Setup (using CMake) and doing the full tutorial, starting with First steps with SeqAn.

In contrast to the Tutorials (which are expected to be useful for all developers), the How-Tos contain more advanced or specific guides. If you have previous experience with SeqAn2 or SeqAn1, have a look at Porting from SeqAn2.

The SeqAn Cookbook contains a listing of code snippets, or recipes that might prove helpful once you have finished the full tutorial and you are implementing your own code. When you are looking for some inspiration on how to perform a particular task or when you searching for something you already know - its on the tip of your tongue - but you can't remember the syntax, take a look here.

Before you publish and/or redistribute software based on SeqAn, please read through the notes on Copyright and Citing. There are few requirements beyond proper attribution, but this requirement we take seriously as it is the basis of acquiring funding for the future development and maintenance of SeqAn.

Resources outside of this web-site that might be useful:

The project homepage with news and application pages.
The GitHub repository with issue tracker and downloads.

Some notes on using this documentation

We use doxygen to generate our documentation. It may not be the most beautiful system, but it works quite well in practice. If you spot any dead links in the documentation, please open an issue at our bug-tracker (see above) or directly submit a pull request fixing the problem.

The documentation is versioned together with the library, see https://docs.seqan.de for release-specific documentation builds. The tutorial on Setting up library tests contains instructions for setting up local documentation builds.

Since doxygen does not support many modern C++ features, some parts of the documentation may not describe the interfaces completely. In particular, many constraints are only expressed verbally in the documentation of an interface and not as part of that interface's code. Also C++ concepts are currently called "interfaces" throughout the documentation.