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https://github.com/seqan/seqan3

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.
https://github.com/seqan/seqan3

bioinformatics blast cpp-concepts cpp17 cpp20 fasta fastq fm-index modern samtools seqan sequence-alignment sequence-analysis

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The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

Lists

README 

        



# SeqAn3 -- the modern C++ library for sequence analysis



[![build status][1]][2]

[![codecov][3]][4]

[![license][5]][6]

[![latest release][7]][8]

[![platforms][9]][10]

[![start][11]][12]

[![twitter][13]][14]



[1]: https://img.shields.io/github/actions/workflow/status/seqan/seqan3/ci_linux.yml?branch=main&style=flat&logo=github&label=SeqAn3%20CI "Open GitHub actions page"

[2]: https://github.com/seqan/seqan3/actions?query=branch%3Amain

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[4]: https://codecov.io/gh/seqan/seqan3

[5]: https://img.shields.io/badge/license-BSD-green.svg "Open Copyright page"

[6]: https://docs.seqan.de/seqan3/main_user/about_copyright.html

[7]: https://img.shields.io/github/release/seqan/seqan3.svg "Get the latest release"

[8]: https://github.com/seqan/seqan3/releases/latest

[9]: https://img.shields.io/badge/platform-linux%20%7C%20bsd%20%7C%20osx-informational.svg "Read more about our API"

[10]: https://docs.seqan.de/seqan3/main_user/about_api.html

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[12]: https://github.com/seqan/seqan3/stargazers

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[14]: 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/seqan3/main_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)                           | ≥ 11     | no other compiler is currently supported!   |

|**build system**   | [CMake](https://cmake.org)                           | ≥ 3.5    | optional, but recommended                   |

|**required libs**  | [SDSL](https://github.com/xxsds/sdsl-lite)           | ≥ 3.0.3  |                                             |

|**optional libs**  | [cereal](https://github.com/USCiLab/cereal)          | ≥ 1.3.1  | required for serialisation and CTD support  |

|                   | [zlib](https://github.com/madler/zlib)               | ≥ 1.2    | required for `*.gz` and `.bam` file support |

|                   | [bzip2](https://www.sourceware.org/bzip2)            | ≥ 1.0    | required for `*.bz2` file support           |



## Usage



We recommend that you use CMake to build your project:



  * [Setup-Tutorial](https://docs.seqan.de/seqan3/main_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++20 mode

    * Macros indicating the presence of zlib and bzip2 (set only if actually available in your paths!)

  * The command could look like this:

```sh

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](https://raw.githubusercontent.com/seqan/seqan3/main/test/documentation/.vercel/powered-by-vercel.svg)](https://vercel.com/?utm_source=seqan&utm_campaign=oss)



Vercel is kind enough to sponsor our documentation preview-builds within our pull requests. Check them out!