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

+----------------------------------------------------------------------------------------------------+ | ATTENTION: SeqAn3 is out and hosted in a different repository: https://github.com/seqan/seqan3 | +----------------------------------------------------------------------------------------------------+ | All new applications should be based on SeqAn3 and all existing applications that receive updates | | should be ported. | +----------------------------------------------------------------------------------------------------+

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.

License

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.

Prerequisites

Linux, MacOS, FreeBSD:

• GCC ≥ 5 [limited GCC-4.9 support on Linux]
• Clang/LLVM ≥ 3.6 [limited Clang-3.5 support on Linux]
• Intel Compiler ≥ 17.0.0 on Linux Windows:
• Visual C++ ≥ 14.0 / Visual Studio ≥ 2015
• Intel Compiler ≥ 17.0.0 / Visual Studio ≥ 2015u2
• Clang/C2 ≥ 3.8.0 / Visual Studio ≥ 2015u3 [experimental, requires CMake ≥ 3.6]

Architecture support:

• Intel/AMD platforms, including optimisations for modern instruction sets (POPCNT, SSE4, AVX2, AVX512)
• All Debian release architectures supported, including most ARM and all PowerPC platforms.

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/>_

Contact

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