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#Created 28/11/2014
#Christophe Antoniewski, CNRS/University Pierre et Marie Curie, [e-mail]
# inspired from the oases wrapper developped by Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter 

Oases optimiser

This Galaxy tool is intended to provide a crude but effective method of producing semi-optimised transcriptome assemblies.
It operates by performing a number of user defined Velvet assemblies upon which Oases is then run.
The results of all of these runs are then put through a final Oases step where they act as scaffolds for the main assembly.
Note that this wrapper is designed to focused on small RNA reads from small RNA sequencings and will run velvetg with kmers ranging from 11 to 35 
Prerequisites:

1. Enclosed scripts
2. package_ged_velvet and package_ged_oases dependency packages

Limitations:

This is a crude optimisation step which DOES NOT try to evaluate the quality of each assembly or map to any reference cDNA.