ASFV Pangenome Analysis

Goal

Create and compare the phylogenetic trees produces from:

1. Whole genome alignment: provides the most comprehensive view
2. B646L (p72) gene alignment: most common gene used for genotyping
3. B602L (CVR) gene alignment: a 400bp region within the relatively conserved central 125-kb region
4. E183L (p54) gene: used as an auxiliary index

TODO

• Retrieve all ASFV assemblies from NCBI
• Data processing
• Run phylogenetic inference
• Identify polymorphisms and structural variants
• Subset the genome and create a pangenome

Workflow

1. Retrieve all ASFV assemblies from NCBI

• the initial search was conducted by passing in "African swine fever virus" as the -query parameter of the esearch tool
• a total of of 348 genomes were retrieved on December 5, 2024
• the genome, cds, and annotation files were included in the download

2. Data processing

• filter for the following gene sequences using bedtools and save as a FASTA file:
  • B646L
  • B602L
  • E183L

3. Run phylogenetic inference

• construct a tree using the whole genome alignment, as well as the three other genes used to genotype ASFV
• visualize tree using ggtree

4. Identify polymorphisms and structural variants

• conduct variant calling to the whole genome alignment

5. Subset the genome and create a pangenome

• subsetted data must include at least one representative from each produced clade