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Fast generation of a core genome among bacterial strains

Project description

install with bioconda


  1. Create a new conda environment (optional, but strongly recommended)
conda env create -n centreseq python=3.6
conda activate centreseq
  1. Install via bioconda
conda install -c bioconda centreseq


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

  centreseq builds an annotated core genome using assemblies as input.

  --version   Print the version and exit.
  --citation  Print the citation for this software and exit.
  --help      Show this message and exit.

  core  Given an input directory containing assemblies, establishes a core
  tree  Produces output for phylogenetic tree software


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.

Project details

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