centreseq 0.2.3

Fast generation of a core genome among bacterial strains

External Dependencies

The following must be available in your $PATH. These programs will be automatically installed with the conda package.

• Prokka
• mmseqs2
• seqkit
• muscle

Installation

1. Create a new conda environment (optional, but strongly recommended)

conda env create -n centreseq python=3.6

2. Install via bioconda

conda install -c bioconda centreseq  # Coming soon

Usage

Usage: centreseq [OPTIONS] COMMAND [ARGS]...

  centreseq builds an annotated core genome using assemblies as input.

Options:
  --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