Workflow for de novo transcriptome + GO + DE, what you recommend ?

[Romualdo]

Hi, I'm working with non reference models and I'm in search of a good workflow for de novo assembly, mapping, GO annotation, Differential Gene Expression and outputing in graphics. Its preferable something close to a all-in-one solution, I know all true all-in-one probably be commercial, I give a look in to geneious, someone used to it ? It gives nice results ?

I tried SOAPdenovo-trans, but I don't know what mapper I should use with it.
Tried trinotate too, it worked well for me, I generated the .sqlite, and used the sqlitebrowser to navigate it, but the trinotateweb that come with the trinotate seems poor about graphic output.

Suggestions will be very appreciated.