GraTools: A Pangenome GFA Toolkit

Available Subcommands

The gratools command provides an overview of all available subcommands, organized into logical sections.

Command Reference

For detailed information on each command, including all options and examples, please see the individual documentation pages:

Core Commands * gratools index: Pre-processes a GFA file for all other operations. * gratools stats: Calculates and displays a wide range of statistics about the graph.

GFA Content Information * gratools list_samples (You’ll need to create this page): Lists all sample names in the GFA. * gratools list_chr (You’ll need to create this page): Lists all chromosomes/contigs per sample.

GFA Data Extraction * gratools extract_subgraph: Extracts a subgraph in GFA format based on a genomic region. * gratools get_fasta: Extracts sequences in FASTA format for a specific region.

GFA Analysis * gratools core_dispensable_ratio: Calculates the ratio of core and dispensable segments. * gratools depth_nodes_stat: Displays statistics about segment sharing across samples. * gratools specific_groups_sample: Identifies segments shared by or specific to defined sample groups. * gratools get_segments_by_depth: Lists segments based on how many samples share them.