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Description
\n\nHiMMe 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.
\n\nInstallation
\n\n1. Clone the repository:
\n\ngit clone git@github.com:jordiabante/HiMMe.git
\n\n2. Add the bin folder in the repository to your path variable by adding the following line to the `.bashrc` (`.bash_profile` in Mac) file:
\n\nexport PATH="path/to/bin:$PATH"
\n\n3. If the machine running the code is Machintosh install coreutils (sudo port install coreutils) as well as: sed, gzip, grep, getopt, mysql, openssl, readline, boost, zlib. Add the following line to the `.bashrc` (`.bash_profile` in Mac) file:
\n\nexport PATH="/opt/local/bin:$PATH"
\n\nexport PATH="/opt/local/libexec/gnubin:$PATH"
\n\nDependancies
\n\n1. bash{pv}
\n\n2. bash{xargs}
\n\n3. perl{Algorithm::Combinatorics}
\n\n\n\n
Content
\n\n1. Every folder (`script_name`) will contain the following files and directories:
\n\n1. `sript_name.sh`: bash script
\n\n2. `main/`
\n\n* `main.sh`: bash script to try the command with toy example.
\n\n* Files required for the toy example.
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