Tool for the rapid inference of O-serogroup and PFGE pattern for Shiga toxin-producing E. coli
- Linux OS
- Python >= 3.7.4
- Scikit-learn >= v.0.22.1
- Pandas >= v1.0.1
- Numpy >= v1.18.1
- Mash >= v2.1
- Download repository from github
- Unzip repository and enter directory
cd pfgeBLAST/
- Untar directory containing pre-generated models
tar -xzvf SavedModels.tar.gz
- Copy desired paired-end FASTQ files into directory "InputFiles". Multiple file pairs can be copied here if running in batch.
- Run program executable: predict_pfge.py with appropriate flag options
python predict_pfge.py -m </path/to/mash-executable> -o </path/to/desired/output-directory>