pfgeBLAST

Tool for the rapid inference of O-serogroup and PFGE pattern for Shiga toxin-producing E. coli

Required software and libraries

• Linux OS
• Python >= 3.7.4
• Scikit-learn >= v.0.22.1
• Pandas >= v1.0.1
• Numpy >= v1.18.1
• Mash >= v2.1

Quick start

1. Download repository from github
2. Unzip repository and enter directory

cd pfgeBLAST/

3. Untar directory containing pre-generated models

tar -xzvf SavedModels.tar.gz

4. Copy desired paired-end FASTQ files into directory "InputFiles". Multiple file pairs can be copied here if running in batch.
5. 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>