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Peer-reviewedCC BY 4.0Emerging Infectious Diseases

Alignment-Free Tool for Assemblies and Reads in Genomic Surveillance of Tuberculosis

  • Paula Ruiz-Rodriguez
  • Mireia Coscollá
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Abstract

Whole-genome sequencing strengthens tuberculosis surveillance, but incomplete lineage schemes can misclassify isolates. We developed Pathotypr, an alignment-free tool for assemblies and reads, using 2,145 markers derived from 26,813 genomes. Across 88,071 samples, Pathotypr improved concordance, expanded uncommon lineage coverage, and detected resistance markers, supporting molecular epidemiology and public health surveillance.

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Cite

BibTeXRIS
BibTeX
@article{ruizrodriguez2026alignmentfree,
  title = {{Alignment-Free Tool for Assemblies and Reads in Genomic Surveillance of Tuberculosis}},
  author = {Paula Ruiz-Rodriguez and Mireia Coscollá},
  journal = {Emerging Infectious Diseases},
  year = {2026},
  month = oct,
  doi = {10.3201/eid3211.261074},
  url = {https://doi.org/10.3201/eid3211.261074},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Alignment-Free Tool for Assemblies and Reads in Genomic Surveillance of Tuberculosis
AU  - Paula Ruiz-Rodriguez
AU  - Mireia Coscollá
PY  - 2026
DA  - 2026/10/30
JO  - Emerging Infectious Diseases
DO  - 10.3201/eid3211.261074
UR  - https://doi.org/10.3201/eid3211.261074
AB  - Whole-genome sequencing strengthens tuberculosis surveillance, but incomplete lineage schemes can misclassify isolates. We developed Pathotypr, an alignment-free tool for assemblies and reads, using 2,145 markers derived from 26,813 genomes. Across 88,071 samples, Pathotypr improved concordance, expanded uncommon lineage coverage, and detected resistance markers, supporting molecular epidemiology and public health surveillance.
SN  - 1080-6040
SN  - 1080-6059
ER  -