This repository generates a heatmap that shows the percent nucleotide identity for genes among different coronaviruses. That heatmap is rendered interactively at https://jbloomlab.github.io/CoV_identities/identities.html.
The code to generate the heatmap is run by a snakemake pipeline in Snakefile in this repository.
To run the code, first build and activate the conda environment in environment.yml, and then simply run snakemake -j 1.
The pipeline works by obtaining the full genomes for the coronaviruses specified in config.yaml. It then builds a full-genome multiple-sequence alignment, and computes percent identities for each gene using the gene boundaries defined in config.yaml.
It then uses altair to generate an interactive heatmap which is rendered via GitHub pages.
The numerical data in the heatmap are in results/identities/identities.csv.
The code is written by Jesse Bloom.