SeqAn3 -- the modern C++ library for sequence analysis
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 | ≥ 11 | no other compiler is currently supported! |
| build system | CMake | ≥ 3.5 | optional, but recommended |
| required libs | SDSL | ≥ 3.0.3 | |
| 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.
Quick-Setup without CMake:
- Clone the repository with submodules:
git clone --recurse-submodules https://github.com/seqan/seqan3.git - Add the following to your compiler invocation:
- the include directories of SeqAn and its dependencies
- C++20 mode
- Macros indicating the presence of zlib and bzip2 (set only if actually available in your paths!)
- The command could look like this:
g++-11 -O3 -DNDEBUG -Wall -Wextra \ -std=c++20 \ -I /path/to/seqan3/include \ -isystem /path/to/seqan3/submodules/sdsl-lite/include \ -isystem /path/to/seqan3/submodules/cereal/include \ -DSEQAN3_HAS_ZLIB=1 -DSEQAN3_HAS_BZIP2=1 \ -lz -lbz2 -pthread \ your_file.cpp
Sponsorships
Vercel is kind enough to sponsor our documentation preview-builds within our pull requests. Check them out!