Examples and Workflows

Some example use cases and workflows for vConTACT3.

The "standard" run (with defaults)

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

The "standard" run (showing defaults)

vcontact3 run --nucleotide genomes.fna --output results_dir --db-domain "prokaryotes" --db-version 228 --db-path /path/to/download/location

Specifying different database versions

As mentioned elsewhere, users can specify which version of the database they wish to use, as well as the path they downloaded the database to.

vcontact3 run run --nucleotide genomes.fna --output results_dir --db-domain "prokaryotes" --db-version 228 --db-path /path/to/download/location