SARS2SpikeMut

This repository contains the following files:

• Snakefile: main workflow to pre-process SARS-CoV-2 GISAID spike protein sequences.
• scripts: analysis scripts for this project.
• data: GISAID sequencing data, reference SARS-CoV-2 Spike protein sequence and experimental data for this project.

How to use:

1. Download SARS-CoV-2 Spike protein sequence from GISAID database (data/prot/spikeprot0705/README.txt).

2. Install the environment:

• python packages:
  • pysam (0.15.4)
  • snakemake (5.4.4)
• R packages:
  • readxl (1.3.1)
  • readr (1.3.1)
  • ggplot2 (3.3.0)
  • Biostrings (2.54.0)
  • BiocParallel (1.20.1)
  • ComplexHeatmap (2.2.0)
  • plotrix (3.8-2)

3. Use snakemake program to run the Snakefile file to perform the sequence preprocessing steps.

4. Use R program to run the scripts/plot_variants.R to plot the results.

Developer

• Dehe Wang