Phylogenomic analysis of all available COVID-19 genomes and its influence on mortality

Package information

Python 3.7.4

• pandas 1.0.5
• biopython 1.77

CODE IMPLEMENTATION

1. Data_filt.py : The python script performs the data cleaning and writes the cleaned data to a new file. This code gets rid of NAs and unknowns from the clinical dataset. The dataset originally contained 4592 samples which after running the python script were 3620.

• Input: The script takes input the GISAID clinical data containing all samples, along with the complete GISAID genomic data for 4592 samples.
• Output: Two files containing filtered samples.