dezordi / sars-cov-2_tools

The published study can be accessed on https://www.mdpi.com/1999-4915/12/12/1414

SARS-CoV-2_tools

This repository stores in house scripts used to automatize some routine tasks with SARS-CoV-2 genomes. Almos all scripts here part of the principle that the genomes used as input have the same pattern of names that are present on GISAID. CSV files were updated on 23 December 2020.

Dependencies

The scripts were built on python 3.6.5+ and have these dependencies:

• argparse;
• biopython;
• pandas.

Recomended lectures

• Pangolin : To understand the lineages pattern.
• Issues with hCoV-19 sequencing data : To understand the sites present on algn_mask.py
• GISAID information : To access the most update hCoV-19 genomic information.

Disclaimer

• If you use one of these scripts, please reference this repository;
• Fell free to commit changes that make the code more efficient or cleaner.
• This script will continue to be developed to englobe other functions.
• More information, Click here!