Attribution

Original ReSeq

ReSeq was created by Stephan Schmeing and Mark D. Robinson at the University of Zurich.

• Paper: Schmeing, S., Robinson, M.D. ReSeq simulates realistic Illumina high-throughput sequencing data. Genome Biology 22, 67 (2021). DOI: 10.1186/s13059-021-02265-7
• Original repository: github.com/schmeing/ReSeq

What Changed in ReSeq2

ReSeq2 is a maintained continuation of the original project. The core simulation algorithms remain the same; the surrounding infrastructure has been modernized:

• C++20 migration --- Updated language standard with modern concurrency (std::jthread, std::scoped_lock), smart pointers, and std::format-ready code
• Modernized CMake build --- CMake 3.16+ with external dependency management via FetchContent and find_package() fallback, replacing vendored copies
• CI/CD pipeline --- GitHub Actions with multi-compiler builds (GCC 13 + Clang 17), ASan/UBSan sanitizers, and automated code coverage
• Expanded test suite --- Golden-file regression tests, component-level unit tests, and integration coverage
• Binary/text profile conversion --- New convertProfile command for portable profile sharing across architectures
• Code quality tooling --- clang-format, clang-tidy, ruff, and pre-commit hooks enforcing consistent style
• Python plotting tools --- Restructured as an installable Python package with type checking and unit tests

Included Libraries

ReSeq2 includes or depends on the following open-source libraries:

Library	License	Inclusion
SeqAn 2.5.2	BSD 3-Clause	FetchContent / find_package()
GoogleTest	BSD 3-Clause	FetchContent
NLopt	MIT	FetchContent
skewer	MIT	Vendored with local modifications (see skewer/MODIFICATIONS.md)

Acknowledgments

ReSeq2 builds on the excellent scientific work of Stephan Schmeing and Mark D. Robinson. Their original implementation of the multi-dimensional probability estimation and realistic read simulation remains the foundation of this tool.