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# SeqAn3 -- the modern C++ library for sequence analysis
[](https://github.com/seqan/seqan3/actions)
[](https://codecov.io/gh/seqan/seqan3)
[](https://docs.seqan.de/seqan/3-master-user/about_copyright.html)
[](https://github.com/seqan/seqan3/releases/latest)
[](https://docs.seqan.de/seqan/3-master-user/about_api.html)
[](https://github.com/seqan/seqan3/stargazers)
[](https://twitter.com/seqanlib)
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](https://docs.seqan.de/seqan/3-master-user/) 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](https://gcc.gnu.org) | ≥ 7 | no other compiler is currently supported! |
|**build system** | [CMake](https://cmake.org) | ≥ 3.4 | optional, but recommended |
|**required libs** | [SDSL](https://github.com/xxsds/sdsl-lite) | ≥ 3 | |
| | [Range-V3](https://github.com/ericniebler/range-v3) | ≥ 0.11.0 | |
|**optional libs** | [cereal](https://github.com/USCiLab/cereal) | ≥ 1.2.3 | required for serialisation and CTD support |
| | [zlib](https://github.com/madler/zlib) | ≥ 1.2 | required for `*.gz` and `.bam` file support |
| | [bzip2](http://www.bzip.org) | ≥ 1.0 | required for `*.bz2` file support |
## Usage
We recommend that you use CMake to build your project:
* [Setup-Tutorial](https://docs.seqan.de/seqan/3-master-user/setup.html)
* 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++17 mode with concepts support
* Macros indicating the presence of zlib and bzip2 (set only if actually available in your paths!)
* The command could look like this:
```sh
g++-7 -O3 -DNDEBUG -Wall -Wextra \
-std=c++17 -fconcepts \
-I /path/to/seqan3/include \
-isystem /path/to/seqan3/submodules/range-v3/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 -lstdc++fs -pthread \
your_file.cpp
```
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