Commands

Panacus commands:

• render: Render an html report from one or more JSON result files
  • takes the output of panacus report --json
  • can be used to concatenate multiple reports into a single HTML file
• report: Create an html report from a YAML config file
  • can output intermediate json using --json
  • placeholders in the YAML ({{MY_KEY}}) can be replaced using -r MY_KEY=replacement_value. With this a single YAML file can be used to analyze multiple graphs (see also example/html_report.md)
• hist: Calculate coverage histogram, table output of !Hist
• growth: Calculate growth curve from coverage histogram [aliases: histgrowth], table output of !Growth
• info: Return general graph and paths info, table output of !Info
• ordered-histgrowth: Calculate growth curve based on group file order (if order is unspecified, use path order in GFA), table output of !OrderedGrowth
• table: Compute coverage table for count type
  • Table mostly used for debugging purporses, this can get very large
• node-distribution: Return the list of bins with there coverages, log10-lengths and log10-sizes. Due to this being the values for the centers of the hexagons shown in the html plot and not real values, some values might be negative. Table output of !NodeDistribution
• similarity: Compute coverage table for count type, table output of !Similarity
• coverage-colors: Create a csv with colors assigned to nodes by Coverage
  • Can be used in viewers such as Bandage and strangepg to visualize nodes by their coverage
  • The lighter an node is the more often it occurs in a path
  • Nodes that are just used a single time are colored in red to highlight them
• section-growth: Calculate growth curve for sections of paths, table output of !SectionGrowth
• help: Print this message or the help of the given subcommand(s)