Docs / About
Citation
If you use Recore, please cite:
Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality control of pangenome presence/absence matrices. In preparation.
@misc{recore,
author = {Ruiz-Rodriguez, Paula and Coscolla, Mireia},
title = {Recore: post-hoc rescue and quality control of pangenome
presence/absence matrices},
year = {2026},
note = {In preparation},
howpublished = {\url{https://github.com/PathoGenOmics-Lab/recore}}
}The software is archived on Zenodo. Cite doi:10.5281/zenodo.23448590 for Recore in general (it resolves to the latest version), or the version you ran, such as doi:10.5281/zenodo.23448591 for 1.0.0:
@software{recore_software,
author = {Ruiz-Rodriguez, Paula and Coscolla, Mireia},
title = {Recore},
version = {1.0.0},
year = {2026},
publisher = {Zenodo},
doi = {10.5281/zenodo.23448591},
url = {https://doi.org/10.5281/zenodo.23448591}
}Please also cite the tools Recore depends on for the run you report:
- minimap2, for every sequence search: Li H. (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34(18):3094-3100.
- MMseqs2, if you used
--nsc-engine mmseqs2: Steinegger M, Soeding J. (2017). MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nature Biotechnology 35:1026-1028. - the pangenome tool that produced the input matrix, for example Panaroo: Tonkin-Hill G, et al. (2020). Producing polished prokaryotic pangenomes with the Panaroo pipeline. Genome Biology 21:180.
Contact#
Paula Ruiz-Rodriguez, paula.ruiz.rodriguez@csic.es
PathoGenOmics Lab, github.com/PathoGenOmics-Lab
License#
GNU Affero General Public License v3.0 (AGPL-3.0-only). See LICENSE.