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        "author": "['Forest Dussault', 'Adrian Verster', 'Nicholas Petronella']",
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        "description": "[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/centreseq/README.html)\n\n\n### Installation\n1. Create a new conda environment (*optional, but strongly recommended*)\n\n```\nconda env create -n centreseq python=3.6\nconda activate centreseq\n```\n\n2. Install via bioconda\n```\nconda install -c bioconda centreseq\n```\n\n### Usage\n```\nUsage: centreseq [OPTIONS] COMMAND [ARGS]...\n\n  centreseq builds an annotated core genome using assemblies as input.\n\nOptions:\n  --version   Print the version and exit.\n  --citation  Print the citation for this software and exit.\n  --help      Show this message and exit.\n\nCommands:\n  core  Given an input directory containing assemblies, establishes a core\n        genome\n  tree  Produces output for phylogenetic tree software\n```\n\n### Issues\nThe conda distribution might have an issue installing the correct version of `minced`,\n a Prokka dependency, so you might need to run the following command within your conda environment after installing centreseq:\n\n`conda install minced`\n\n### External Dependencies\n\nThese programs will be automatically installed with the conda package.\n\n- [Prokka](https://github.com/tseemann/prokka)\n- [MMseqs2](https://github.com/soedinglab/MMseqs2)\n- [SeqKit](https://github.com/shenwei356/seqkit)\n- [MUSCLE](https://www.drive5.com/muscle/)\n- [SNP-sites](https://github.com/sanger-pathogens/snp-sites)\n- [cyvcf2](https://github.com/brentp/cyvcf2)",
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