Getting Started

This chapter gives you the necessary steps to get started with SeqAn:

  • Necessary Prerequisites
  • Installing SeqAn from Subversion
  • Creating a first build.
  • Creating your own first application.

Use the following links to select your target operating system and IDE/build system. The bold items show the recommended build system for the given platforms.


Mac Os X


Getting started on Linux using



Getting started on Mac Os X using



Getting started on Windows using

Visual Studio 8, 9, 10, 11

MinGW + Eclipse

Click "more" for details on the supported development platforms.

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Relevant How-Tos

Although slightly more advanced than "getting started", the following How-Tos apply to setting up your build environment:

How To: Use Parallel Build Directories
With CMake, it is easy to create multiple build directories and thus different Makefile configurations or project files for different IDEs. This is important to know if you want to have debug and release Makefiles next to each other. Also, if you want to have build files for more than one Visual Studio version, then this How-To is for you!
How To: Use SeqAn In Your Projects
This How-To explains how to use SeqAn in your projects with your own build system. It deals with the precompiler defines to set, paths etc.
How To: Use The Latest Clang In XCode
Clang is a new C++ compiler with very nice error output. This How-To describes how to use the latest in XCode on Mac Os X.
How To: Install Contribs on Windows
Installing and compiling libraries such as zlib or libbz2 on Windows can be tricky. We provide prebuilt binaries which we recommend to use with SeqAn on Windows. This How-To describes how to install them (it's as easy as extracting one ZIP file).