[BioRuby] bio-assembly

Raoul Bonnal bonnalraoul at ingm.it
Thu Jan 13 09:30:03 UTC 2011

great work guys.

I have updated the Plugins' page http://bioruby.open-bio.org/wiki/Plugins#On_Development_Plugins, it's a list/resume with the state of the art of the plugins.

Please let me know if there is something wrong.

In my mind Planned plugins are just ideas not yet coded.

The other are "on going development". I tried to list the plugins in order of creations.

@Jan: Do you plan to release Ensembl API as a  plugin ? I think is't just a matter of rename the gem
@Geroge: To avoid problems, please, yank isoelectric_point from rubygems

I didn't receive any reply from Ricardo H. Ramírez-Gonzalez about samtools-ruby-ffi

Do you think that a separate page would be better?  I think so, u?


On 12/gen/2011, at 19.37, Chase Miller wrote:

> Hi All,
> Quick update on the bio-assembly plugin.
> Francesco has added support for CAF files.  According to his preliminary
> tests it can handle a 27k contig 454 file in about a minute.  He also
> improved the performance overall so now the ace parser can process a 70 mb
> file in about 10 seconds. Nice work!
> If there are any requests for parsers or functionality, let us know.
> source code: https://github.com/chmille4/bioruby-assembly
> <https://github.com/chmille4/bioruby-assembly>usage:
> https://github.com/chmille4/bioruby-assembly#readme
> gem: https://rubygems.org/gems/bio-assembly
> Cheers
> Chase
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