bio-gfastqc

Full description goes here

Note: this software is under active development!

Installation

gem install bio-gfastqc

Usage

require 'bio-gfastqc'

The API doc is online. For more code examples see the test files in the source tree.

Project home page

Information on the source tree, documentation, examples, issues and how to contribute, see

http://github.com/helios/bioruby-gfastqc

The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.

Create a config YAML file

config.yml

it contents is for example:

samples:
  Sample_A: /path_to_sampleA
  Sample_B: /path_to_sampleB

then run the script in the directory of the config.yml file and specify the sub directory for each sampel where is located the result of the FASTQC

ruby gfastqc.rb -a R1 -b R2

in case you have the results of FastQC in a sub folder and you want to keep the definition of the sample independen from it, you can use the step option

ruby gfastqc.rb -a R1 -b R2 --step qc_pre_trimming

Then open index.html in your browser

TODO

• avoid user to specify -a and -b. By default discover zip files and ordering them define the first and second strand.
• ~~package everything as a gem~~
• provide better documentation for installing the gem on multiple system (GNU/Linux, OSX, Windows)

Cite

If you use this software, please cite one of

• BioRuby: bioinformatics software for the Ruby programming language
• Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics

Biogems.info

This Biogem is published at (http://biogems.info/index.html#bio-gfastqc)

Copyright

Copyright (c) 2015 Raoul Jean Pierre Bonnal. See LICENSE.txt for further details.