WOOF

Wonderful O-antigens Operons Finder

Authors:
Oksana Kotovskaia
Ekaterina Marenina
Igor Ostanin
Nadezhda Pavlova
Nikita Vaulin
Independent researchers from Glasgow

Supervisor:
Polina Kuchur, chesnokova@scamt-itmo.ru,
Applied genomics laboratory, ITMO University, Saint-Petersburg, Russia

Overview

O-antigens are essential components of lipopolysaccharides exposed on the surface of bacterial cells, and their diversity has increased significantly over time. The identification of O-antigen operons is crucial for comparative genomics, bacterial identification, epidemiological studies, and vaccine development tasks. Here we introduce WOOF, an automatic pipeline for searching and visualizing O-antigen operons.

Dependencies

• Snakemake manual

Installation

You can get WOOF via GitHub

git clone git@github.com:aglabx/OantigenMiner.git

Then move to the repository directory:

cd OantigenMiner

Usage

Example usage

Write path to fasta file:

data = Path({folder_name})
GENOME = "{file_prefix}"
email = 'myemail@example.com'

Run WOOF:

snakemake -c {threads} --use-conda

Troubleshooting

If you encounter any issues or have questions, you can open an issue on the GitHub page or directly contact the authors for support.

Citation

If you use these tool, please cite as:

• Kotovskaia O., Ostanin I., Marenina E., Pavlova N., Vaulin N. , Kuchur P., Komissarov A. WOOF: Wonderful O-anrtigens Operons Finder. Природа, 2023, 220, 1--128

@article{phandorin2023,
  title={WOOF: Wonderful O-antigens Operons Finder},
  author={Kotovskaia O., Ostanin I., Marenina E., Pavlova N., Vaulin N. , Kuchur P., Komissarov A.},
  journal={Природа},
  year={2023},
  volume={220},
  pages={1--128}
}