50Core genome Subtyping
These instructions will get you a copy of the project up and running on your local machine for development and testing purposes.
module load BBMap/35.92
module load SPAdes/3.9.0
module load Python/3.7
module load ncbi-blast+/LATEST
module load muscle/3.8.425
module load raxml/8.2.9
module load Entrez/E-utilities
module load prodigal/2.63
pip install -r requirements.txt --user
git clone https://git.biotech.cdc.gov/nej1/50scheme.git
cd ~/50scheme/
python pipe1.py ~/50scheme/test1/
This script runs entire pipeline from the beginning and get all output results
*base_dir: type 'pwd' in your home directory(i.e./scicomp/home/youruserid/)
There would be "outputfile" directory at the end of pipeline under "your_home_directory/your_genome_directory" (i.e./scicomp/home/youruserid/test1/outputfile/)
There would be myscript.log in your home directory that you can check when the pipeline started, each step completed, and finished.
Subin Park
APHL fellow at Centers for Disease control and Prevention
Phone : +1 470 725 5110 Email :nej1@cdc.gov