Metadata-Version: 2.4
Name: kleborate
Version: 3.3.0b1
Summary: Kleborate: a tool for typing and screening pathogen genome assemblies
Author-email: Mary Maranga <gathonimaranga@gmail.com>, Ryan Wick <rrwick@gmail.com>, Kathryn Holt <kat.holt@lshtm.ac.uk>
License-Expression: GPL-3.0-or-later
Project-URL: homepage, https://github.com/klebgenomics/Kleborate
Project-URL: documentation, https://kleborate.readthedocs.io/
Project-URL: repository, https://github.com/klebgenomics/Kleborate
Classifier: Development Status :: 4 - Beta
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Classifier: Intended Audience :: Science/Research
Requires-Python: >=3.11
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: biopython==1.81
Requires-Dist: numpy>=1.26.0
Requires-Dist: kaptive
Requires-Dist: rammappy
Provides-Extra: test
Requires-Dist: pytest; extra == "test"
Requires-Dist: pytest-mock; extra == "test"
Dynamic: license-file

<p align="center"><picture><source srcset="images/logo-dark.png" media="(prefers-color-scheme: dark)"><img src="images/logo.png" alt="Kleborate logo" width="400"></picture></p>

Kleborate was primarily developed to screen genome assemblies of _Klebsiella pneumoniae_ and the _Klebsiella pneumoniae_ species complex (KpSC) for:

* Species (e.g. _K. pneumoniae_, _K. quasipneumoniae_, _K. variicola_, etc.)
* _K. pneumoniae_ species complex MLST
* ICEKp associated virulence loci: yersiniabactin (_ybt_), colibactin (_clb_), salmochelin (_iro_), hypermucoidy (_rmp_)
* Virulence plasmid associated loci: salmochelin (_iro_), aerobactin (_iuc_), hypermucoidy (_rmp_, _rmpA2_)
* Antimicrobial resistance determinants: acquired genes, SNPs, gene truncations and intrinsic β-lactamases
* K (capsule) and O antigen (LPS) serotype prediction, via _wzi_ alleles and [Kaptive](https://github.com/klebgenomics/Kaptive)

Kleborate v3 includes a rewrite of the code to (i) replace the use of BLAST with [minimap2](https://lh3.github.io/minimap2/minimap2.html) (faster and less buggy); and (ii) introduce a modular structure making it easy to add new typing modules, including for other species. Currently, functionality for other species is limited to MLST for _Klebsiella oxytoca_ species complex and _Escherichia coli_ but more is in development.

A list of changes from v2 is available in the [documentation](https://kleborate.readthedocs.io/en/latest/index.html#changes-from-v2).

**Documentation**

For information on how to install and run Kleborate v3, please visit the [Docs](https://kleborate.readthedocs.io/en/latest/).

**Citation**

If you use Kleborate, please cite the paper: Lam, MMC. et al. A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex, Nature Communications (2021). https://doi.org/10.1038/s41467-021-24448-3


If you use the Kaptive calls for K and O locus typing please cite: Stanton  et al. Fast and accurate in silico antigen typing with Kaptive 3. Microbial Genomics (2025). https://doi.org/10.1099/mgen.0.000102


If you use the cgMLST and LIN code calls, please cite the paper: Bogaerts et al. MiST: rapid, accurate and flexible (core-genome) multi-locus sequence typing (MLST) allele calling from draft genomes. BMC Genomics (2025). https://doi.org/10.1186/s12864-025-12324-z


For a full list of acknowledgments and citations for third-party tools and databases used by Kleborate, please see the [Docs](https://kleborate.readthedocs.io/en/latest/).
