Pathotypr
Pathotypr is an alignment-free tool for harmonised Mycobacterium tuberculosis complex (MTBC) lineage assignment and resistance genotyping from assemblies and raw reads.
Pathotypr enables rapid, harmonised MTBC lineage assignment and high-confidence resistance screening, supporting near real-time and cross-border tuberculosis surveillance.
Basic Information
| Repository | https://github.com/PathoGenOmics-Lab/pathotypr |
| Documentation | https://pathogenomics-lab.github.io/pathotypr/ |
| Seminar | Paula Ruiz Rodríguez (I2SYSBIO, CSIC) presents the tool Pathotypr |
| Main publication (DOI) | 10.64898/2026.03.24.714002 |
| Contact email | paula.ruiz.rodriguez@csic.es |
| Authors/Maintainers | Paula Ruiz Rodríguez, Mireia Coscolla Devis |
| Type of application | Desktop application, Command line pipeline, Conda package, Galaxy tool |
| Programming languages | RustJavaScript |
| Keywords | Machine Learning in Biology, Genomics, Variant calling, Lineage assignment, Drug resistance, Genomic surveillance |
Technical details
| Input file formats | FASTA, FASTQ, TSV |
| Output file formats | TSV, XLSX |
| Software compatibility | Linux, Mac, Windows |
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| Type of containerization | Conda |
| Wrapper type | None |
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| Citations (last 12 months) | <100 (~0 as of 15/10/2026) |
| Citations (since first release) | <100 (0 as of 15/10/2026) |
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