StrainAnalyze: a user-friendly bioinformatics pipeline used to analyze given identified bacterial strains in short reads. For example, if you have identified strains in short reads using StrainScan, then you can use StrainAnalyze to perform in-depth analysis based on the identified strains and short reads.
Yon can install StrainScan via Anaconda using the commands below:
git clone https://github.com/liaoherui/StrainAnalyze.git
cd StrainAnalyze
conda env create -f environment.yaml
conda activate strainanalyze
python StrainAnalyze.py -h