Installation
- Create a new conda environment (optional, but strongly recommended)
conda env create -n centreseq python=3.6
conda activate centreseq
- Install via bioconda
conda install -c bioconda centreseq
Usage
Usage: centreseq [OPTIONS] COMMAND [ARGS]...
centreseq builds an annotated core genome using assemblies as input.
Options:
--version Print the version and exit.
--citation Print the citation for this software and exit.
--help Show this message and exit.
Commands:
core Given an input directory containing assemblies, establishes a core
genome
tree Produces output for phylogenetic tree software
Issues
The conda distribution might have an issue installing the correct version of minced,
a Prokka dependency, so you might need to run the following command within your conda environment after installing centreseq:
conda install minced
External Dependencies
These programs will be automatically installed with the conda package.
