[BioRuby] BIO-NGS (and Rake/Thor for bioinformatics)

Francesco Strozzi francesco.strozzi at gmail.com
Fri Jan 21 09:41:47 UTC 2011

Hi all,
in the yesterday IRC chat (http://bioruby.org/irc/?date=2011-01) we
discussed about the bio-ngs plugin that Raoul wrote in a previous
Here is the Wiki page on BioRuby describing the general idea for this
plugin: http://bioruby.open-bio.org/wiki/Next_Generation_Sequencing

We want to use wrappers and/or bindings to existing tools like
MAQ,BWA,SAMtools and we want to use Rake or Thor to provide custom
tasks and let the user run NGS analysis. We would like to include also
the possibility to create reports using statsample and rubyvis. Maybe
some aspects are still a bit unclear at the moment (I think we need to
define some sort of guidelines), but I hope we could come up with a
useful (let me use this term) "framework" to run bioinformatics NGS
analyses with Ruby.

Any comment/help/feedback/suggestion is more than welcome!




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