Fast generation of a core genome among bacterial strains
- 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: 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
The conda distribution might have an issue installing the correct version of
a Prokka dependency, so you might need to run the following command within your conda environment after installing centreseq:
conda install minced
These programs will be automatically installed with the conda package.
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