SeqAn3 is the next version of the popular SeqAn template library for the analysis of biological sequences. If you develop applications, we recommend you currently stick to SeqAn2.
SeqAn3 is major redesign of SeqAn and has fundamental changes throughout the codebase. We expect that porting applications from SeqAn2 to SeqAn3 requires substantial work, however by embracing new technologies from C++17 and modern third party libraries, SeqAn3 will be a much improved experience over SeqAn2.
- same design goals as SeqAn2: fast, efficient, extensible C++ header library for sequence analysis
- different design patterns: generic programming via C++ Concepts, encapsulation and members
- modern C++ that relies heavily on C++17, the Concepts TS and Ranges TS
To include SeqAn3 in your app, you need the following:
| requirement | version | comment | |
|---|---|---|---|
| compiler | GCC | ≥ 7 | no other compiler is currently supported! |
| build system | cmake | ≥ 3.4 | optional, but recommended |
| required libs | SDSL | ≥ 3 | succint datastructures |
| Ranges-V3 | == 0.3.* | ranges and views | |
| optional libs | Cereal | ≥ 1.2.3 | serialisation |
| Lemon | ≥ 1.3.1 | graphs, required for MSA |
To build the tests and API documentation, you also need:
| requirement | version | |
|---|---|---|
| build system | cmake | ≥ 3.4 |
| test system | GoogleTest | ≥ 1.8 |
| doc system | Doxygen | ≥ 1.8 |
To use SeqAn3, clone this repository including it's submodules:
git clone --recursive https://github.com/seqan/seqan3.gitSeqAn3 is still a header-only library so it is sufficient to add the include folder to your include path. When building make sure that you add the required parameters:
g++-7 -std=c++17 -fconcepts -I /path/to/seqan3/include -I /path/to/seqan3/submodules/range-v3/include -I /path/to/seqan3/submodules/sdsl-lite/include myfile.cpp- API documentation
- Manual and tutorials (coming soon)