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HiMMe v1.0

Jordi Abante


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  <identifier identifierType="DOI">10.5281/zenodo.49770</identifier>
  <creators>
    <creator>
      <creatorName>Jordi Abante</creatorName>
      <affiliation>Texas A&amp;M University</affiliation>
    </creator>
  </creators>
  <titles>
    <title>HiMMe v1.0</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2016</publicationYear>
  <dates>
    <date dateType="Issued">2016-04-14</date>
  </dates>
  <resourceType resourceTypeGeneral="Software"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/49770</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsSupplementTo">https://github.com/jordiabante/HiMMe/tree/v1.0</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.595012</relatedIdentifier>
  </relatedIdentifiers>
  <version>v1.0</version>
  <rightsList>
    <rights rightsURI="https://opensource.org/licenses/MIT">MIT License</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;&lt;em&gt;Description&lt;/em&gt;&lt;/p&gt;

&lt;p&gt;&lt;em&gt;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.&lt;/em&gt;&lt;/p&gt;

&lt;p&gt;&lt;em&gt;Installation&lt;/em&gt;&lt;/p&gt;

&lt;p&gt;&lt;em&gt;1. Clone the repository:&lt;/em&gt;&lt;/p&gt;

&lt;p&gt;&lt;em&gt;&amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; git clone git@github.com:jordiabante/HiMMe.git&amp;nbsp;&lt;/em&gt;&lt;/p&gt;

&lt;p&gt;&lt;em&gt;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:&lt;/em&gt;&lt;/p&gt;

&lt;p&gt;&lt;em&gt;&amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; export PATH=&amp;quot;path/to/bin:$PATH&amp;quot;&lt;/em&gt;&lt;/p&gt;

&lt;p&gt;&lt;em&gt;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:&lt;/em&gt;&lt;/p&gt;

&lt;p&gt;&lt;em&gt;&amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; export PATH=&amp;quot;/opt/local/bin:$PATH&amp;quot;&lt;/em&gt;&lt;/p&gt;

&lt;p&gt;&lt;em&gt;&amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; export PATH=&amp;quot;/opt/local/libexec/gnubin:$PATH&amp;quot;&lt;/em&gt;&lt;/p&gt;

&lt;p&gt;&lt;em&gt;Dependancies&lt;/em&gt;&lt;/p&gt;

&lt;p&gt;&lt;em&gt;1. bash{pv}&lt;/em&gt;&lt;/p&gt;

&lt;p&gt;&lt;em&gt;2. bash{xargs}&lt;/em&gt;&lt;/p&gt;

&lt;p&gt;&lt;em&gt;3. perl{Algorithm::Combinatorics}&lt;/em&gt;&lt;/p&gt;

&lt;p&gt;&amp;nbsp;&lt;/p&gt;

&lt;p&gt;&lt;em&gt;Content&lt;/em&gt;&lt;/p&gt;

&lt;p&gt;&lt;em&gt;1. Every folder (`script_name`) will contain the following files and directories:&lt;/em&gt;&lt;/p&gt;

&lt;p&gt;&lt;em&gt;&amp;nbsp; 1. `sript_name.sh`: bash script&lt;/em&gt;&lt;/p&gt;

&lt;p&gt;&lt;em&gt;&amp;nbsp; 2. `main/`&lt;/em&gt;&lt;/p&gt;

&lt;p&gt;&lt;em&gt;&amp;nbsp; &amp;nbsp; * `main.sh`: bash script to try the command with toy example.&lt;/em&gt;&lt;/p&gt;

&lt;p&gt;&lt;em&gt;&amp;nbsp; &amp;nbsp; * Files required for the toy example.&lt;/em&gt;&lt;/p&gt;</description>
  </descriptions>
</resource>
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