Extract and Visualize Pangenome Information#

The info subcommand extracts summary information from PPanGGOLiN .h5 pangenome files and generates interactive HTML reports. These reports support quick content comparison of each pangenome.

Info command line usage#

panorama info -i <pangenome_list.tsv> -o <output_directory> [--status] [--content]

Output#

  • status_info.html — Status of pangenome processing steps (annotation, clustering, etc.)

  • content_info.html — Numerical summary: genomes, genes, gene families, modules, etc.

Key options#

Option

Description

–status

Extract and export the status (booleans) of each pangenome.

–content

Extract and export structural and numerical content metrics.

Default: if no flags are provided, both --status and --content are extracted.

Note

--parameters and --metadata are not yet available. Use --status and/or --content for now.

Exploring the Reports#

Status info#

Shows whether each processing step was completed:

Example columns: Genomes_Annotated, Genes_Clustered, RGP_Predicted, etc.

Features:

  • Radio button filters for boolean values.

  • TSV download of filtered results.

Content info#

Displays statistics such as:

  • Number of genes, genomes, gene families, modules.

  • Frequencies and standard deviations.

  • Partition composition (persistent, shell, cloud).

Features:

  • Column visibility toggles.

  • Range sliders for numeric filtering.

  • TSV export of filtered view.