/HiMMe

HiMMe

Primary LanguagePerlMIT LicenseMIT

#HiMMe DOI Description

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.

Installation

  1. Clone the repository:

     git clone git@github.com:jordiabante/HiMMe.git

  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:

     export PATH="path/to/bin:$PATH"

  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:

     export PATH="/opt/local/bin:$PATH"
 export PATH="/opt/local/libexec/gnubin:$PATH"

Dependancies

  1. bash{pv}
  2. bash{xargs}
  3. perl{Algorithm::Combinatorics}

Content

  1. Every folder (script_name) will contain the following files and directories:
  2. sript_name.sh: bash script
  3. main/ * main.sh: bash script to try the command with toy example. * Files required for the toy example.