COVID-19 mortality risk assessment among various age groups using phylogenomic analysis

Python 3.7.4

Package information

• pandas 1.0.5
• biopython 1.77

R

Package information

• ggplot2
• hrbrthemes
• dplyr
• tidyr
• viridis

DATASETS

All datasets for the analysis are avaliable at https://zenodo.org/record/4007666#.X0qEK3UzacC

DATA FILTRATION

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.

PHYLOGENETIC ANALYSIS

The phylogenetic analysis was performed on the https://usegalaxy.org/ server using the filtered genomic datasets for 3620 genomes.
MAFFT was used for multiple sequence alignment with default paramteres, and FASTTREE was used for the phylogenetic tree reconstruction.

OR CALCULATION

To generate the annotations for the tree ORCaD app was used, along with OR calculations
For OR calculations see ORCaD

CONFLICTS

Please contact pawan12394@gmail.com in case of any issues

LICENSE

The project was licensed under the Apache 2.0 license