PyocinTyper

Type pyocins of Pseudomonas aeruginosa.

Dependencies

Nextflow
Install nextflow following the instructions at https://www.nextflow.io/docs/latest/getstarted.html.

cd-hit
Install cd-hit following the instructions at https://github.com/weizhongli/cdhit.

Anaconda
This pipeline is enabled with conda. Install conda at https://anaconda.org/.

All dependencies must be added to path.

Installation

Via github:

git clone https://github.com/GaTechBrownLab/PyocinTyper.git

Via nextflow:

nextflow pull GaTechBrownLab/PyocinTyper

Usage

Basic usage:

nextflow run main.nf -with-conda --pt_option <group|individual> --input_files "./data/*.gbff" --outdir "/results"

Documentation

nextflow run main.nf --help