vConTACT3 run

The run subcommand performs viral genome clustering and taxonomic assignment using nucleotide or protein inputs.

Usage Examples:

Run with nucleotide input:

vcontact3 run --nucleotide genomes.fna --output results_dir

Run with pre-predicted protein inputs:

vcontact3 run --proteins proteins.faa --gene2genome gene2genome.tsv --len-nucleotide genome_lengths.tsv --output results_dir

Customize database domain and exports:

vcontact3 run --nucleotide genomes.fna --db-domain prokaryotes --exports graphml d3js completeness --output results_dir

Command Line Reference:

usage: vcontact3 run [-h] {version,prepare_databases,run} ...