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 paper. 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. Alignment-Free Tool for Assemblies and Reads in Genomic Surveillance of Tuberculosis. Emerg Infect Dis. 2026;32(11):1913-1918. doi: 10.3201/eid3211.261074

BibTeXRISAPA

@article{ruizrodriguez2026pathotypr,
  title   = {Alignment-Free Tool for Assemblies and Reads in Genomic
             Surveillance of Tuberculosis},
  author  = {Ruiz-Rodriguez, Paula and Coscoll{\'a}, Mireia},
  journal = {Emerging Infectious Diseases},
  year    = {2026},
  volume  = {32},
  number  = {11},
  pages   = {1913--1918},
  doi     = {10.3201/eid3211.261074}
}

TY  - JOUR
TI  - Alignment-Free Tool for Assemblies and Reads in Genomic Surveillance of Tuberculosis
AU  - Ruiz-Rodriguez, Paula
AU  - Coscollá, Mireia
JO  - Emerging Infectious Diseases
PY  - 2026
VL  - 32
IS  - 11
SP  - 1913
EP  - 1918
DO  - 10.3201/eid3211.261074
ER  -

Ruiz-Rodriguez, P., & Coscollá, M. (2026). Alignment-free tool for assemblies
and reads in genomic surveillance of tuberculosis. Emerging Infectious
Diseases, 32(11), 1913-1918. https://doi.org/10.3201/eid3211.261074

Already cited the preprint?

The same work was first posted on bioRxiv as Pathotypr: harmonised MTBC lineage assignment and resistance-associated variant detection for genomic surveillance, doi: 10.64898/2026.03.24.714002. Please cite the published article above in new work.

Cite the software and markers¶

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

10.5281/zenodo.19210043

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 0000-0003-0752-0538

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.

Citation¶

Cite the paper¶

Cite the software and markers¶

Authors¶

Licence¶

See also¶