13  classify

The classify subcommand classifies genomes into cliques (k-complete) graphs based on ANI results, generating plots and tabular summaries. This is helpful for circumscribing potentially meaningful groups of genomes that can not be described using traditional taxonomy. The output, including classify plots (JPG, PDF, PNG, SVGZ) and tabular data, is written to outdir directory.

pyani-plus classify Usage

pyani-plus classify [OPTIONS]

13.1 Options

--database: Path to pyANI-plus SQLite3 database. (FILE) [REQUIRED]

--outdir: Output directory. (DIRECTORY) [REQUIRED]

--run-id: Which run from the database. [Defaults to latest.] (INTEGER)

--label: How to label the genomes. [Default: stem.] (md5|filename|stem)

--help, -h: Display usage information for pyani-plus reasume and exit.

13.2 Method parameters

--mode: Classify mode intended to identify cliques within a set of genomes. [Default: identity] (identity|tANI)

--score-edges: How to resolve asymmetrical ANI identity/tANI results for edges in the graph (min, max or mean). [Default: min] (TEXT)

--coverage-edges: How to resolve asymmetrical ANI coverage results for edges in the graph (min, max or mean). [Default: min] (TEXT)

--cov-min: Minimum %coverage for an edge. [Default: 0.5] (\(0.0 \leq x \leq 1.0\) )

--vertical-line: Threshold for red vertical line at identity/tANI. The default is set to 0.95 if --mode is identity and -0.323 if --mode is tANI. (TEXT)