We are working on an article on de novo transcriptome assemblers, and it will be released in following four parts this week. Stay tuned !!
Part 1 - Larger Perspective
Part 2 Trinity and Oases Quick Start Guide
Part 3 Assembly Algorithms of Trinity and Oases
Part 4 Tricks and Tips for Better Results
If you are in a hurry, I also reported an example of our experience with trinity assembler in the forum. It discusses how to run the program, gives some estimates on how much time the program takes to run, RAM size, explains the directory structures, etc.