The info command in PPanGGOLiN enables users to acquire comprehensive insights into the contents and construction process of a pangenome file.

Different types of information can be displayed using various parameters, such as --status, --parameters, --content, and --metadata. When no flag is specified, all available outputs are displayed.

ppanggolin info -p pangenome.h5

The info command generates information in YAML format, displaying the results directly in the standard output without writing to any files.

Overview of info --content Output

The --content option with the info command exposes general statistical data about your pangenome:

  1. General Metrics:

    • Presents a comprehensive count of genes, genomes, gene families, and edges within the pangenome graph.

  2. Partitioned Metrics:

    • Provides detailed information for each partition, including gene counts and presence thresholds for persistent, shell, and cloud families among genomes.

  3. Number of Partitions:

    • Indicates the total count of partitions in the pangenome.

  4. Genome Fluidity:

    • If computed through the ‘metrics’ command, displays genome fluidity values across all partitions and within each partition.

  5. Regions of Genomic Plasticity (RGPs):

    • Exhibits counts of Regions of Genomic Plasticity (RGPs) and spots of insertion if predicted using commands such as ‘all’, ‘panrgp’, ‘rgp’, or ‘spot’.

  6. Modules:

    • Shows counts of modules and associated gene families if predicted using commands like ‘module’, ‘panmodule’, or ‘all’. Additionally, provides partition composition percentages for these modules.

Overview of info --parameters Output

This option displays the PPanGGOLiN parameters used at each step of the analysis. The output can be utilized as a configuration file for other PPanGGOLiN commands to replicate the same parameters. Refer here for more details about configuration files.

Overview of info --status Output

Using this option, users can check what analysis have been conducted to obtain the pangenome file.

Overview of info --metadata Output

When metadata has been added to the pangenome elements, this option showcases which elements possess metadata and their respective sources. Find more details on metadata here.