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HiMMe v1.0

Jordi Abante


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{
  "description": "<p><em>Description</em></p>\n\n<p><em>HiMMe is a computational biology tool that applies hidden Markov models (HMM) to assess NGS data reliability and is able to detect errors and repair them.</em></p>\n\n<p><em>Installation</em></p>\n\n<p><em>1. Clone the repository:</em></p>\n\n<p><em>&nbsp; &nbsp; &nbsp; &nbsp; git clone git@github.com:jordiabante/HiMMe.git&nbsp;</em></p>\n\n<p><em>2. Add the bin folder in the repository to your path variable by adding the following line to the `.bashrc` (`.bash_profile` in Mac) file:</em></p>\n\n<p><em>&nbsp; &nbsp; &nbsp; &nbsp; export PATH=&quot;path/to/bin:$PATH&quot;</em></p>\n\n<p><em>3. If the machine running the code is Machintosh install coreutils (sudo port install coreutils) as well as: sed, gzip, grep, getopt, mysql, openssl, readline, boost, zlib. Add the following line to the `.bashrc` (`.bash_profile` in Mac) file:</em></p>\n\n<p><em>&nbsp; &nbsp; &nbsp; &nbsp; export PATH=&quot;/opt/local/bin:$PATH&quot;</em></p>\n\n<p><em>&nbsp; &nbsp; &nbsp; &nbsp; export PATH=&quot;/opt/local/libexec/gnubin:$PATH&quot;</em></p>\n\n<p><em>Dependancies</em></p>\n\n<p><em>1. bash{pv}</em></p>\n\n<p><em>2. bash{xargs}</em></p>\n\n<p><em>3. perl{Algorithm::Combinatorics}</em></p>\n\n<p>&nbsp;</p>\n\n<p><em>Content</em></p>\n\n<p><em>1. Every folder (`script_name`) will contain the following files and directories:</em></p>\n\n<p><em>&nbsp; 1. `sript_name.sh`: bash script</em></p>\n\n<p><em>&nbsp; 2. `main/`</em></p>\n\n<p><em>&nbsp; &nbsp; * `main.sh`: bash script to try the command with toy example.</em></p>\n\n<p><em>&nbsp; &nbsp; * Files required for the toy example.</em></p>", 
  "license": "http://www.opensource.org/licenses/MIT", 
  "creator": [
    {
      "affiliation": "Texas A&M University", 
      "@type": "Person", 
      "name": "Jordi Abante"
    }
  ], 
  "url": "https://zenodo.org/record/49770", 
  "codeRepository": "https://github.com/jordiabante/HiMMe/tree/v1.0", 
  "datePublished": "2016-04-14", 
  "version": "v1.0", 
  "@context": "https://schema.org/", 
  "identifier": "https://doi.org/10.5281/zenodo.49770", 
  "@id": "https://doi.org/10.5281/zenodo.49770", 
  "@type": "SoftwareSourceCode", 
  "name": "HiMMe v1.0"
}
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