[BioRuby] BioRuby HTSeq-like

Francesco Strozzi francesco.strozzi at gmail.com
Tue Jan 18 20:55:20 UTC 2011

Hi BioRuby people,
just wondering if something similar exists for BioRuby (is a package
to work and manipulate next-gen sequencing data, in Python):


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?



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