.. image:: https://readthedocs.io/projects/seqan/badge/?version=develop :target: https://seqan.readthedocs.io/en/develop?badge=develop :alt: Documentation Status

SeqAn - The Library for Sequence Analysis

What Is SeqAn?

SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. Our library applies a unique generic design that guarantees high performance, generality, extensibility, and integration with other libraries. SeqAn is easy to use and simplifies the development of new software tools with a minimal loss of performance.


The SeqAn library itself, the tests and demos are licensed under the very permissing 3-clause BSD License. The licenses for the applications themselves can be found in the LICENSE files.


Linux, Mac OSX, FreeBSD:

  • GCC ≥ 4.9 [GCC ≥ 5 recommended]
  • Clang/LLVM ≥ 3.5
  • Intel Compiler ≥ 16.0.2 Windows:
  • Visual C++ ≥ 14.0 / Visual Studio ≥ 2015
  • Intel Compiler ≥ 16.0.3 / Visual Studio ≥ 2015u2
  • Clang/C2 ≥ 3.8.0 / Visual Studio ≥ 2015u3 [experimental, requires CMake ≥ 3.6]

Architecture support:

  • 32bit and 64bit Intel/AMD officially supported
  • 64bit is highly recommended and some parts of SeqAn are optimized for POPCNT, SSE4 and/or AVX2 instruction sets available on newer CPUs
  • many other architectures, including ARM, PowerPC and Sparc64 work, but receive less testing and optimizations

To build tests, demos, and official SeqAn applications you also need:

  • CMake ≥ 3.0 [CMake ≥ 3.4 recommended]

Some of the official applications might have additional requirements or work only on a subset of platforms.

Documentation Resources

  • Getting Started <http://seqan.readthedocs.io/en/master/Tutorial/GettingStarted>_
  • Manual <http://seqan.readthedocs.io/en/master>_
  • Tutorial <http://seqan.readthedocs.io/en/master/index.html#tutorials>_
  • How-Tos <http://seqan.readthedocs.io/en/master/Tutorial/HowTo>_
  • API Documentation (stable) <http://docs.seqan.de/seqan/master/>_


  • Mailing List <https://lists.fu-berlin.de/listinfo/seqan-dev#subscribe>_
  • GitHub Project (issues, source code) <https://github.com/seqan/seqan>_

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