To cite systemPipeR in publications, please use the first reference below, which describes the current systemPipeR workflow management system. The second reference is the original systemPipeR publication.

Zhang L, Cassol D, Gongol B, Girke T (2026). “systemPipeR: a multipurpose workflow management system for reproducible data analysis.” NAR Genomics and Bioinformatics, 8(2), lqag032. doi:10.1093/nargab/lqag032. https://doi.org/10.1093/nargab/lqag032.

Backman TWH, Girke T (2016). “systemPipeR: NGS workflow and report generation environment.” BMC Bioinformatics, 17(1), 388. doi:10.1186/s12859-016-1241-0. https://doi.org/10.1186/s12859-016-1241-0.

Corresponding BibTeX entries:

  @Article{,
    title = {systemPipeR: a multipurpose workflow management system for
      reproducible data analysis},
    author = {Le Zhang and Daniela Cassol and Brendan Gongol and Thomas
      Girke},
    journal = {NAR Genomics and Bioinformatics},
    year = {2026},
    volume = {8},
    number = {2},
    pages = {lqag032},
    doi = {10.1093/nargab/lqag032},
    url = {https://doi.org/10.1093/nargab/lqag032},
  }

  @Article{,
    title = {systemPipeR: NGS workflow and report generation
      environment},
    author = {Tyler W. H. Backman and Thomas Girke},
    journal = {BMC Bioinformatics},
    year = {2016},
    volume = {17},
    number = {1},
    pages = {388},
    doi = {10.1186/s12859-016-1241-0},
    url = {https://doi.org/10.1186/s12859-016-1241-0},
  }