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HiMMe v1.0

Jordi Abante


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    <subfield code="a">HiMMe v1.0</subfield>
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    <subfield code="u">http://www.opensource.org/licenses/MIT</subfield>
    <subfield code="a">MIT License</subfield>
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    <subfield code="a">&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;</subfield>
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    <subfield code="a">https://github.com/jordiabante/HiMMe/tree/v1.0</subfield>
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