There is a newer version of this record available.

Software Open Access

HiMMe v1.0

Jordi Abante


Dublin Core Export

<?xml version='1.0' encoding='utf-8'?>
<oai_dc:dc xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:oai_dc="http://www.openarchives.org/OAI/2.0/oai_dc/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd">
  <dc:creator>Jordi Abante</dc:creator>
  <dc:date>2016-04-14</dc:date>
  <dc:description>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.</dc:description>
  <dc:identifier>https://zenodo.org/record/49770</dc:identifier>
  <dc:identifier>10.5281/zenodo.49770</dc:identifier>
  <dc:identifier>oai:zenodo.org:49770</dc:identifier>
  <dc:relation>url:https://github.com/jordiabante/HiMMe/tree/v1.0</dc:relation>
  <dc:relation>doi:10.5281/zenodo.595012</dc:relation>
  <dc:rights>info:eu-repo/semantics/openAccess</dc:rights>
  <dc:rights>http://www.opensource.org/licenses/MIT</dc:rights>
  <dc:title>HiMMe v1.0</dc:title>
  <dc:type>info:eu-repo/semantics/other</dc:type>
  <dc:type>software</dc:type>
</oai_dc:dc>
54
6
views
downloads
All versions This version
Views 549
Downloads 60
Data volume 2.5 MB0 Bytes
Unique views 519
Unique downloads 40

Share

Cite as