Bioinformatics. Aggregate FastQC (quality control for Next Generation Sequencing -NGS-) results from many different samples in a single web page, with charts and tables organized and simplified. The main goal is to speed up the communication process with colleagues (PIs, Biologists, BioInformaticians).
Note: this software is under active development!
gem install bio-gfastqcrequire 'bio-gfastqc'The API doc is online. For more code examples see the test files in the source tree.
Note: at this time there is not a real API, it will follow.
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
gfastqc -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
gfastqc -a R1 -b R2 --step qc_pre_trimming
Then open index.html in your browser
Pipengine, https://github.com/fstrozzi/bioruby-pipengine, a simple launcher for complex biological pipelines. Because we are developing it we found usefult to reuse some best practices from it. An example is the -s/--step options which let you select the sample inner directory from which grab the FastQC results. In the current examples we defined just samples and their absolut path, but following the Pipengine directives it is necessary to define another tag:
output: /path/where_the_pipe_engine_data_are_processed_and_saved
to reuse that tag from gfastqc the user can simply select the option
-p/--pipengine
the software will look for the results of single fastqc applied to the different samples in the output directory.
read output tag from sample config file (YAML)add reference to pipengine- 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)
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
This Biogem is published at (http://biogems.info/index.html#bio-gfastqc)
Copyright (c) 2015 Raoul Jean Pierre Bonnal. See LICENSE.txt for further details.