[BioRuby] BioRuby HTSeq-like

Raoul Bonnal bonnalraoul at ingm.it
Thu Jan 20 10:35:58 UTC 2011

Hi folks,
Yesterday I met Francesco in my lab and was a wonderful opportunity to exchange ideas and thoughts.

About Fancesco's mail I think that we could grab inspiration from Galaxy/BioPython (http://main.g2.bx.psu.edu/) , they did a very good work on wrapping the common software for crunching NGS data.

So my input is, let's start wrapping them and possibly opening a bioruby-ngs project on github:
https://github.com/helios/bioruby-ngs (just the repo :-))

reading around  http://seqanswers.com/forums/showthread.php?t=2461 sometimes there is the need to split and distribute the computation:
there are different possibilities, but splitting the fastq file and at the same time enabling the multithreading seems to be the best option; if you have suggestions please comment. 

Thanks to Goto san, fastq support is on 
Thanks to Pjotr, GFF3 support is on
Thanks to Chase and Fancesco, CAF and Ace support is on
For plotting as we said one possibility is http://rubyvis.rubyforge.org/  from Claudio Bustos but if you have better alternatives... please discuss.
About  statistics please join http://groups.google.com/group/sciruby-dev 

Having this tools in our arsenal is useful and strategical for founding.

I would say 

PS: Please clone and add your name to the list of the authors if you want to join into this project.

PS: if someone is using SGE what do you think about http://gridengine.info/2010/12/24/goodbye-grid-engine ?

On 18/gen/2011, at 21.55, Francesco Strozzi wrote:

> Hi BioRuby people,
> just wondering if something similar exists for BioRuby (is a package
> to work and manipulate next-gen sequencing data, in Python):
> http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html
> Many features could be implemented or are already available for
> BioRuby....these are the basics:
> - Getting statistical summaries about the base-call quality scores to
> study the data quality.
> - Calculating a coverage vector and exporting it for visualization in
> a genome browser.
> - Reading in annotation data from a GFF file.
> - Assigning aligned reads from an RNA-Seq experiments to exons and genes.
> Particularly, the plotting functions to explore and assess quality
> data seems very interesting.
> If nothing similar exists for BioRuby, I think we should discuss about
> coding a BioRuby "NextGenSequencing" plugin, to provide the same
> functionalities and also to add something new as well....
> What do you think?
> Cheers
> --
> Francesco
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby


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