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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
Last synced: 27 days ago
JSON representation
The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.
- Host: GitHub
- URL: https://github.com/seqan/seqan3
- Owner: seqan
- License: other
- Created: 2016-04-04T12:39:15.000Z (over 8 years ago)
- Default Branch: main
- Last Pushed: 2024-05-16T15:02:09.000Z (6 months ago)
- Last Synced: 2024-05-18T22:55:53.586Z (6 months ago)
- Topics: bioinformatics, blast, cpp-concepts, cpp17, cpp20, fasta, fastq, fm-index, modern, samtools, seqan, sequence-alignment, sequence-analysis
- Language: C++
- Homepage: https://www.seqan.de
- Size: 20.7 MB
- Stars: 389
- Watchers: 24
- Forks: 80
- Open Issues: 29
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.md
- License: LICENSE.md
- Code of conduct: CODE_OF_CONDUCT.md
Awesome Lists containing this project
- Awesome-Bioinformatics - SeqAn - The modern C++ library for sequence analysis. (Package suites)
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
[3]: https://codecov.io/gh/seqan/seqan3/branch/main/graph/badge.svg?token=BH1FQiBBle "Open Codecov page"
[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
[11]: https://img.shields.io/github/stars/seqan/seqan3.svg?style=social "See who starred us"
[12]: https://github.com/seqan/seqan3/stargazers
[13]: https://img.shields.io/twitter/follow/SeqAnLib.svg?label=follow&style=social "Follow us on Twitter"
[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
```