During a course in Fall 2012, I tested using CLC Bio’s Genomic’s workbench for an RNASeq analysis project.
CLC Bio has an educational program that for $100/student each student can get a copy of the CLC Genomics workbench that is good for one semester or one year (I forget which). This also allows each student to have a long-term copy of the CLC bio main workbench. This workbench will not be updated.
Nice graphical user interface
Lots of built in functionality with lots of power
Can go from data analysis to primer design all in the same environment
Can design workflow pipelines
Hard to export data to other programs
Not intuitive how to adapt system to do something else