SeqAn3 -- the modern C++ library for sequence analysis
February 28, 2026 · View on GitHub
SeqAn3 is the new version of the popular SeqAn template library for the analysis of biological sequences. It enables the rapid development of high-performance solutions by providing generic algorithms and data structures for:
- sequence representation and transformation
- full-text indexing and efficient search
- sequence alignment
- input/output of common file formats
By leveraging Modern C++ it provides unprecedented ease-of-use without sacrificing performance.
Please see the online documentation for more details.
Quick facts
- C++ header-only library: easy to integrate with your app & easy to distribute
- liberal open source license: allows integration with any app or library, requires only attribution
- very high code quality standards: >97% unit test coverage, performance regression tests, ...
- extensive API documentation & tutorials: more lines of documentation than lines of code
- aims to support any 64-bit architecture running Linux/POSIX; currently big-endian CPU architectures like s390x are less supported
Dependencies
| requirement | version | comment | |
|---|---|---|---|
| compiler | GCC | ≥ 12 | |
| Clang | ≥ 17 | tested with -stdlib=libc++ | |
| IntelOneAPI | ≥ 2024.0 | ||
| build system | CMake | ≥ 3.20 | optional, but recommended |
| optional libs | cereal | ≥ 1.3.1 | required for serialisation and CTD support |
| zlib | ≥ 1.2 | required for *.gz and .bam file support | |
| bzip2 | ≥ 1.0 | required for *.bz2 file support |
Usage
We recommend that you use CMake to build your project:
- Setup-Tutorial
- Using CMake guarantees that all optional dependencies are automatically detected and activated.