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Software Open Access

HiMMe v1.0

Jordi Abante

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:

  1. `sript_name.sh`: bash script

  2. `main/`

    * `main.sh`: bash script to try the command with toy example.

    * Files required for the toy example.

Files (418.1 kB)
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HiMMe-v1.0.zip
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