PneumoSerotyping

PneumoSerotyping is a pipeline for identifying Streptococcus pneumoniae serotypes using long reads data. Dependency:

1. Python (https://packages.ubuntu.com/) Install: sudo apt install python3
2. Flye (https://github.com/fenderglass/Flye) Install: conda install bioconda::flye
3. Mash version 2.3 (or 2.0+) https://github.com/marbl/Mash Install: conda install bioconda::mash
4. Numpy (http://www.scipy.org/scipylib/download.html) Install: pip install numpy
5. pandas (https://pandas.pydata.org/) Install: pip install pandas
6. SQLite3 (https://www.sqlite.org/index.html) Install: sudo apt install sqlite3
7. PneumoKITy (https://github.com/CarmenSheppard/PneumoKITy?tab=readme-ov-file) Install: git clone https://github.com/CarmenSheppard/PneumoKITy