Citation¶

How to cite pathotypr, the DOIs for the software and marker panels, and the licence.

If pathotypr contributed to your results, please cite the preprint. Citing the software DOI as well lets readers retrieve the exact marker panels and model you ran against.

Cite the paper¶

Ruiz-Rodriguez P, Coscollá M. Pathotypr: harmonised MTBC lineage assignment and resistance-associated variant detection for genomic surveillance. bioRxiv (2026). doi: 10.64898/2026.03.24.714002

BibTeXRISAPA

@article{ruizrodriguez2026pathotypr,
  title   = {Pathotypr: harmonised MTBC lineage assignment and
             resistance-associated variant detection for genomic surveillance},
  author  = {Ruiz-Rodriguez, Paula and Coscoll{\'a}, Mireia},
  journal = {bioRxiv},
  year    = {2026},
  doi     = {10.64898/2026.03.24.714002}
}

TY  - JOUR
TI  - Pathotypr: harmonised MTBC lineage assignment and resistance-associated
      variant detection for genomic surveillance
AU  - Ruiz-Rodriguez, Paula
AU  - Coscollá, Mireia
JO  - bioRxiv
PY  - 2026
DO  - 10.64898/2026.03.24.714002
ER  -

Ruiz-Rodriguez, P., & Coscollá, M. (2026). Pathotypr: harmonised MTBC lineage
assignment and resistance-associated variant detection for genomic
surveillance. bioRxiv. https://doi.org/10.64898/2026.03.24.714002

Cite the software and markers¶

The archived release, including the marker panels and the trained model, has its own DOI:

10.5281/zenodo.19210044

Record the version you ran

Marker panels change between releases, so a lineage or resistance call is only reproducible alongside the version that produced it. pathotypr --version prints it, and every output file records it in its header.

The repository also ships a CITATION.cff file, so GitHub's Cite this repository button always returns an up-to-date reference.

Authors¶


Paula Ruiz-Rodriguez	ORCID 0000-0003-0727-5974
Mireia Coscollá	ORCID 0000-0003-2078-1032

Institute for Integrative Systems Biology (I²SysBio), CSIC and University of Valencia.

Licence¶

pathotypr is released under the GNU Affero General Public License v3.0. You may use, modify and redistribute it, including in a service offered over a network, provided derivative works stay under the same licence and their source remains available.