Project

bio-gngm

0.0
No commit activity in last 3 years
No release in over 3 years
bio-gngmdanmaclean/bioruby-gngmHomepageDocumentationSource CodeBug TrackerWiki
Identify causative mutations in a model genome from NGS reads using the NGM method.
2005
2006
2007
2008
2009
2010
2011
2012
2013
2014
2015
2016
2017
2018
2019
2020
2021
2022
2023
2024
 Popularity
Downloads
13,276
Stars
2
Forks
1
Watchers
3
 Releases
Current version
0.2.1
Total releases
3
First release
2012-03-19
Latest release
2012-12-06
 Development
Primary Language
Ruby
Licenses
MIT
Average date of last 50 commits
2012-06-26
Reverse Dependencies
0

 Dependencies

Development

bio
>= 1.4.2
bio-samtools
>= 0.5.0
bundler
~> 1.0.0
jeweler
>= 0
rcov
>= 0
rdoc
>= 0
rinruby
>= 2.0.2
shoulda
>= 0

Runtime

bio
>= 1.4.2
bio-samtools
>= 0.5.0
rinruby
>= 2.0.2
 Project Readme

bio-gngm¶ ↑

Ruby Gem for performing identification of causative mutations in a model genome using the NGM method.

A Bio::Util::Gngm object represents a single region on a reference genome that is to be examined using the NGM technique described in Austin et al (2011) bar.utoronto.ca/ngm/description.html and onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2011.04619.x/abstract;jsessionid=F73E2DA628523B26205297CEE95526DA.d02t04 Austin et al (2011) Next-generation mapping of Arabidopsis genes Plant Journal 67(4):7125-725 .

Bio::Util::Gngm provides methods for finding SNPs, small INDELS and larger INDELS, creating histograms of polymorphism frequency, creating and clustering density curves, creating signal plots and finding peaks. The ratio of reference-agreeing and reference-differing reads can be specified.

Background¶ ↑

The basic concept of the technique is that density curves of polymorphism frequency across the region of interest are plotted and analysed. Each curve is called a thread, as it represents a polymorphism that was called with a statistic within a certain user-specified range, eg if a SNP was called with 50% non-reference bases from sequence reads (say all A), and 50% reference reads (all T) then a discordant chastity statistic (ChD) of 0.5 would be calculated and assigned to that SNP. Depending on the width and slide of the windows the user had specified, the frequency of SNPs with ChD in the specified range would be drawn in the same density curve.

Finding regions enriched in a target ChD and depleted in others can point to causative mutations.

Contributing to bio-gngm¶ ↑

  • Check out the latest master to make sure the feature hasn’t been implemented or the bug hasn’t been fixed yet

  • Check out the issue tracker to make sure someone already hasn’t requested it and/or contributed it

  • Fork the project

  • Start a feature/bugfix branch

  • Commit and push until you are happy with your contribution

  • Make sure to add tests for it. This is important so I don’t break it in a future version unintentionally.

  • Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.

Copyright¶ ↑

Copyright © 2011 Dan MacLean. See LICENSE.txt for further details.