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PPanGGOLiN container

Main tool: PPanGGOLiN

Code repository: https://github.com/labgem/PPanGGOLiN

Basic information on how to use this tool:

  • executable: ppanggolin
  • help: --help
  • version: --version
  • description: |

PPanGGOLiN builds pangenomes through a graphical model and a statistical method to partition gene families in persistent, shell and cloud genomes.

Additional information:

PPanGGOLiN only creates the pangenome graphs. It is recommended to use another tool to visualize them. Please read https://github.com/labgem/PPanGGOLiN/wiki for more information.

Full documentation: https://github.com/labgem/PPanGGOLiN/wiki

Example Usage

ppanggolin annotate --fasta organisms.fasta.list --output output 

# many of the commands manipulate the 'pangenome.h5' file in place
ppanggolin cluster -p pangenome.h5
ppanggolin graph -p pangenome.h5 
ppanggolin partition -p pangenome.h5
ppanggolin draw -p pangenome.h5 --ucurve   

# there are some human-readable files that can be generated as well
ppanggolin write -p pangenome.h5 --stats --output stats