skani

The skani subcommand processes genome files from the indir directory to perform skani analysis, and logs comparison and run data in a local SQLite3 database.

Tippyani-plus skani Usage

pyani-plus skani [OPTIONS] FASTA 

Arguments

fasta: Directory of FASTA files (extensions .fas, .fasta, .fna). (PATH) [REQUIRED]

Options

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

--create-db: Create database if does not exist.

--name: Run name. [Default: “N genomes using METHOD”] (TEXT)

--executor: How should the internal tools be run? [Default: local] (local|slurm)

--help, -h: Display usgae information for pyani-plus anib.

Method parameters

--nide: Selects one of the skani presets. [Default: fast] (choice: fast|medium|slow|small-genomes )

Debugging

--temp: Directory to use for intermediate files, which for debugging purposes will not be deleted. For clusters this must be on a shared drive. Default behaviour is to use a system specified temporary directory (specific to the compute-node when using a cluster) and remove this afterwards. (Directory)

--wtemp: Directory to use for temporary workflow coordination files, which for debugging purposes will not be deleted. For clusters this must be on shared drive. Default behaviour is to use a system specified temporary directory (for the local executor) or a temporary directory under the present direct (for clusters), and remove this afterwards. (Directory)