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# SeqAn - The Library for Sequence Analysis
[![build status][1]][2]
[![license][3]][4]
[![latest release][5]][6]
[![platforms][7]][8]
[![start][9]][10]
[![twitter][11]][12]
[1]: https://img.shields.io/github/actions/workflow/status/seqan/seqan/ci_linux.yml?branch=main&style=flat&logo=github&label=SeqAn%20CI "Open GitHub actions page"
[2]: https://github.com/seqan/seqan/actions?query=branch%3Amain
[3]: https://img.shields.io/badge/license-BSD-green.svg "Open license file"
[4]: https://github.com/seqan/seqan/blob/main/LICENSE
[5]: https://img.shields.io/github/release/seqan/seqan.svg "Get the latest release"
[6]: https://github.com/seqan/seqan/releases/latest
[7]: https://img.shields.io/badge/platform-linux%20%7C%20bsd%20%7C%20osx%20%7C%20win-informational.svg "Open our API documentation"
[8]: https://docs.seqan.de/seqan/main/
[9]: https://img.shields.io/github/stars/seqan/seqan.svg?style=social "See who starred us"
[10]: https://github.com/seqan/seqan/stargazers
[11]: https://img.shields.io/twitter/follow/SeqAnLib.svg?label=follow&style=social "Follow us on Twitter"
[12]: https://twitter.com/seqanlib
| **NOTE <br> [SeqAn3 is out and hosted in a different repository](https://github.com/seqan/seqan3)** |
|:----------------------------------------------------------------------------------------------------:|
| We recommend using SeqAn3 for new applications. |
## 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 permissive 3-clause BSD License.
The licenses for the applications themselves can be found in the LICENSE files.
## Prerequisites
Older compiler versions might work but are neither supported nor tested.
### Linux, macOS, FreeBSD
* GCC ≥ 13
* Clang/LLVM ≥ 18
* Intel oneAPI C++ Compiler 2025.0 (IntelLLVM)
### Windows
* Visual C++ ≥ 17.0 / Visual Studio ≥ 2022
### 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.
### Build system
* To build tests, demos, and official SeqAn applications you also need CMake ≥ 3.12.
Some official applications might have additional requirements or only work on a subset of platforms.
## Documentation Resources
* [Getting Started](https://seqan.readthedocs.io/en/main/Tutorial/GettingStarted)
* [Manual](https://seqan.readthedocs.io/en/main)
* [Tutorial](https://seqan.readthedocs.io/en/main/index.html#tutorials)
* [How-Tos](https://seqan.readthedocs.io/en/main/Tutorial/HowTo)
* [API Documentation (stable)](https://docs.seqan.de/seqan/main/)
### Building a SeqAn Application (*apps* Directory)
To build an application from the `apps` directory, you can pass `-DSEQAN_BUILD_SYSTEM=APP:<APPNAME>` to CMake. \
`<APPNAME>` is the name of one of the subdirectories in the `apps` directory. \
In the examples below, we build the `mason2` application.
```bash
# To clone a specific release, replace `main` with the desired tag, e.g., `seqan-v2.5.1`.
git clone --depth 1 --branch main https://github.com/seqan/seqan.git
cd seqan
mkdir -p build
cmake -S . -B build -DCMAKE_BUILD_TYPE=Release -DSEQAN_BUILD_SYSTEM=APP:mason2
cmake --build build --parallel
ls build/bin # Binaries are available in the `build/bin` directory.
```
## Contact
* [Mailing List](https://lists.fu-berlin.de/listinfo/seqan-dev#subscribe)
* [GitHub Project (issues, source code)](https://github.com/seqan/seqan)
|
