Kaptive

GitHub Repo stars License PyPI - Python Version Conda

About

Kaptive is a system for surface polysaccharide typing from bacterial genome sequences. It consists of two main components:

  1. Curated reference databases of surface polysaccharide gene clusters (loci).
  2. A command-line interface (CLI) with three modes:
    • assembly: surface polysaccharide typing from assemblies
    • extract: extract features from Kaptive databases in different formats
    • convert: convert Kaptive results to different formats

Kaptive can be found:

For full documentation, including install and usage instructions, click here.

Citation

  • If you use Kaptive in your research, please cite2.
  • If you use the Klebsiella K or O locus databases, please cite3 and4.
  • If you use Kaptive Web, please cite5.
  • If you use the A. baumannii K or OC locus database(s) in your research please cite6 and7.

Tutorial

Step-by-step video and documented tutorials are available, covering:

  • Kaptive's features and their scientific rationale
  • How to run Kaptive
  • Examples, illustrating how to run and interpret results
  • Further investigations (e.g. exploring novel loci, IS insertions)

!!! note The tutorials are based on Kaptive 2.0, but the principles are similar for Kaptive 3.0.

People

Contact Kelly and Tom for help with Kaptive, or to report bugs or request features.

References

  1. Van Der Graaf-van Bloois, L., Chen, H., Wagenaar, J.A., Zomer, A.L., 2023. Development of Kaptive databases for Vibrio parahaemolyticus O- and K-antigen genotyping. Microbial Genomics 9. https://doi.org/10.1099/mgen.0.001007 ↩

  2. Stanton TD, Hetland MAK, Löhr IH, Holt KE, Wyres KL. Fast and Accurate in silico Antigen Typing with Kaptive 3. 2025 Microbial Genomics 11(6):001428. https://doi.org/10.1099/mgen.0.001428 ↩

  3. Wyres, K.L., Wick, R.R., Gorrie, C., Jenney, A., Follador, R., Thomson, N.R., Holt, K.E., 2016. Identification of Klebsiella capsule synthesis loci from whole genome data. Microbial Genomics 2, e000102. https://doi.org/10.1099/mgen.0.000102 ↩

  4. Lam, M.M.C., Wick, R.R., Judd, L.M., Holt, K.E., Wyres, K.L., 2022. Kaptive 2.0: updated capsule and lipopolysaccharide locus typing for the Klebsiella pneumoniae species complex. Microbial Genomics 8. https://doi.org/10.1099/mgen.0.000800 ↩

  5. Wick, R.R., Heinz, E., Holt, K.E., Wyres, K.L., 2018. Kaptive Web: User-Friendly Capsule and Lipopolysaccharide Serotype Prediction for Klebsiella Genomes. Journal of Clinical Microbiology 56, 10.1128/jcm.00197-18. https://doi.org/10.1128/jcm.00197-18 ↩

  6. Wyres, K.L., Cahill, S.M., Holt, K.E., Hall, R.M., Kenyon, J.J., 2020. Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive. Microbial Genomics 6. https://doi.org/10.1099/mgen.0.000339 ↩

  7. Cahill, S.M., Hall, R.M., Kenyon, J.J., 2022. An update to the database for Acinetobacter baumannii capsular polysaccharide locus typing extends the extensive and diverse repertoire of genes found at and outside the K locus. Microbial Genomics 8. https://doi.org/10.1099/mgen.0.000878 ↩

Project links

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  • Released:
Newer release available (3.3.1)

1 maintainer

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Avatar for tomdstanton from gravatar.com tomdstanton

Credits

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Author: Tom Stanton

GitHub Statistics

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The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License

GNU General Public License v3 (GPLv3) (GNU GENERAL PUBLIC LICENSE)

Requires

Python >=3.9

Tags

bioinformatics microbiology serotyping

Classifiers

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