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Citing AMAP

Ruiz-Rodriguez, P., & Coscolla, M. (2026). AMAP (Version 1.0.1) [Computer software]. https://doi.org/10.5281/zenodo.8024446

@software{Ruiz-Rodriguez_AMAP_2026,
  author = {Ruiz-Rodriguez, Paula and Coscolla, Mireia},
  doi = {10.5281/zenodo.8024446},
  license = {GPL-3.0},
  month = apr,
  title = {{AMAP}},
  url = {https://github.com/PathoGenOmics-Lab/AMAP},
  version = {1.0.1},
  year = {2026}}

The repository also carries a CITATION.cff, which GitHub reads to offer a formatted citation from the sidebar.

Authors#

Paula Ruiz-Rodriguez and Mireia Coscolla

I²SysBio, University of Valencia-CSIC, FISABIO Joint Research Unit Infection and Public Health, Valencia, Spain.

Cite the tools too#

AMAP orchestrates other people's work. If a result depends on one of these, cite it as well.

Tool	What it does here
Nextflow	Runs the pipeline
Bakta	Baseline annotation
Miniprot	Reference proteome alignment
eggNOG-mapper	Functional annotation
Diamond	Duplication searches
pangene	Pangenome graph
pathotypr	MTBC lineage typing

The exact version of each one used by a given run is recorded in results/pipeline_info/software_versions.yml.

Reference data#

The MTBC reference files bundled in the container come from public repositories. The pathotypr lineage markers are archived on Zenodo under 10.5281/zenodo.19210044, and Mycobrowser functional categories come from mycobrowser.epfl.ch.

Licence#

AMAP is released under the GPL-3.0 licence. See LICENSE.

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