mcpalumbo/corecruncher repository overview

⁠CoreCruncher Docker Image

This Docker image runs CoreCruncher⁠, a tool designed to build the core genome of prokaryotic genomes.

⁠Quick Start

To run CoreCruncher with the default settings (which uses USEARCH) and generate output in the current working directory, use the following command:

docker run --rm --volume "$PWD":/data mcpalumbo/corecruncher:1 /CoreCruncher/corecruncher_master.py -in {directory with .faa files} -out /data -ref {name of reference .faa file} -align mafft

This command will output results to the /data directory in the container and in your current working path.

⁠Additional Options

For more information on available parameters and options, run:

docker run --rm --volume "$PWD":/data mcpalumbo/corecruncher:1 /CoreCruncher/corecruncher_master.py -h

This command will display the help documentation for CoreCruncher, showing all available flags and their functions.