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README.md  view on Meta::CPAN

    * [Ancient systems and versions of perl](#ancient-systems-and-versions-of-perl)
    * [Running the tests](#running-the-tests)
    * [Versions of software we test against](#versions-of-software-we-test-against)
  * [Usage](#usage)
  * [License](#license)
  * [Feedback/Issues](#feedbackissues)
  * [Citation](#citation)
  * [Further Information](#further-information)

## Introduction
Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka) and calculates the pan genome.  Using a standard desktop PC, it can analyse datasets with thousands of samples, something whic...

## Installation
Roary has the following dependencies:

### Required dependencies
* [bedtools](https://bedtools.readthedocs.io/en/latest/)
* [cd-hit](http://weizhongli-lab.org/cd-hit/)
* [ncbi-blast+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download)
* [mcl](https://micans.org/mcl/)
* [parallel](https://www.gnu.org/software/parallel/)

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