Pitfalls of bacterial pan-genome analysis approaches

a case study of Mycobacterium tuberculosis and two less clonal bacterial species

Marin, Maximillian G Conceptualization; Data curation; Formal analysis; Investigation; Methodology; Project administration; Resources; Software; Supervision; Validation; Visualization; Writing - original draft; Writing - review & editing
Quinones-Olvera, Natalia Formal analysis; Methodology; Visualization; Writing - review & editing
Wippel, Christoph Data curation; Formal analysis; Visualization
Behruznia, Mahboobeh Conceptualization; Data curation; Formal analysis; Methodology; Validation; Writing - review & editing
Jeffrey, Brendan M Data curation; Investigation; Resources
Harris, Michael Data curation; Resources
Mann, Brendon C Data curation; Investigation; Writing - review & editing
Rosenthal, Alex Funding acquisition
Jacobson, Karen R Funding acquisition
Warren, Robin M Funding acquisition
Li, Heng Formal analysis; Investigation; Supervision; Writing - review & editing
Meehan, Conor J Project administration; Supervision; Writing - review & editing
Farhat, Maha R Conceptualization; Data curation; Formal analysis; Funding acquisition; Investigation; Methodology; Project administration; Supervision; Visualization; Writing - original draft; Writing - review & editing

Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, United States
Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, United States
Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, United States
Department of Biosciences, Nottingham Trent University, Nottingham, NG1 4FQ, United Kingdom
Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, 20892, United States
Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, 20892, United States
Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Stellenbosch, Western Cape, 7602, South Africa
Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, 20892, United States
Division of Infectious Diseases, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, United States
Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Stellenbosch, Western Cape, 7602, South Africa
Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, United States
Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, United States
Broad Institute of Harvard and MIT, Cambridge, MA 02142, United States
Department of Biosciences, Nottingham Trent University, Nottingham, NG1 4FQ, United Kingdom
Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, 2000, Belgium
Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, United States
Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA 02114, United States

Corresponding authors. Maximillian G. Marin, Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, United States. E-mail: [email protected]; Maha R. Farhat, Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, United States. E-mail: [email protected]

Received April 22, 2024

Received in revised form December 31, 2024

Accepted May 07, 2025

Revised May 28, 2025

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

Bioinformatics 41(5), May 2025. | DOI: 10.1093/bioinformatics/btaf219