There is a newer version of this record available.

Software Open Access

HiMMe v1.0

Jordi Abante


Citation Style Language JSON Export

{
  "publisher": "Zenodo", 
  "DOI": "10.5281/zenodo.49770", 
  "title": "HiMMe v1.0", 
  "issued": {
    "date-parts": [
      [
        2016, 
        4, 
        14
      ]
    ]
  }, 
  "abstract": "<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>", 
  "author": [
    {
      "given": "", 
      "family": "Jordi Abante"
    }
  ], 
  "version": "v1.0", 
  "type": "article", 
  "id": "49770"
}
70
6
views
downloads
All versions This version
Views 7018
Downloads 60
Data volume 2.5 MB0 Bytes
Unique views 6718
Unique downloads 40

Share

Cite as