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