centreseq 0.3.0

Fast generation of a core genome among bacterial strains

Installation

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

conda env create -n centreseq python=3.6
conda activate centreseq

2. 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.

• Prokka
• MMseqs2
• SeqKit
• MUSCLE
• SNP-sites
• cyvcf2