Plot genome alignment figure tool

:warning: I have developed a new python package pyGenomeViz that enables visualization of genome alignment by progressiveMauve. I recommend using that for now.

Automated genome alignment figure plot tool using progressiveMauve & genoPlotR.

Genome alignment figure is output from input genome sequence files.
Genbank or Fasta format genome sequence is available as input.

Fig. 6 E.coli genome alignment visualization result example

Requirements

This tool is implemented in Python3 & R (Tested on Ubuntu20.04).

Following dependencies are required.

• BioPython (Python library)

  pip install biopython
  

• genoPlotR, ape, ade4 (R library)

  install.packages(c("genoPlotR", "ape", "ade4"), dependencies = TRUE)
  

• progressiveMauve (External binary)

  sudo apt install progressivemauve
  

Command Usage

Basic Command

python plot_genome_align_fig.py -i [genome_files_dir] -t [species_tree_file] -o [outdir] 

Options

-h, --help      show this help message and exit
-i , --indir    Input genome Genbank or Fasta files directory (*.gbk|*.fa)
-o , --outdir   Output directory
-t , --tree     Newick species tree file
--width         Plot width inch (Default: 10)
--height        Plot height inch (Default: 7)
--tree_width    Plot tree width inch (Default: 2)

:warning: Input file name and input newick species tree leaf name must be match.

Example Command

Example of 6 E.coli species genome (Genbank)

python plot_genome_align_fig.py -i example/ecoli/genbank -t example/ecoli/ecoli.nwk -o ecoli_plot1

genoPlotR_genome_align.jpg

Example of 6 E.coli species genome (Fasta)

Change width, height, tree_width parameters.

python plot_genome_align_fig.py -i example/ecoli/fasta -t example/ecoli/ecoli.nwk -o ecoli_plot2 --width 12 --height 5 --tree_width 4

genoPlotR_genome_align.jpg

Example of 7 Mycoplasma species genome

python plot_genome_align_fig.py -i example/mycoplasma/genbank -t example/mycoplasma/mycoplasma.nwk -o mycoplasma_plot

genoPlotR_genome_align.jpg