I'm new to the 454 pipeline racket and have been looking around for the best pipeline to use to analyze the 16s sequences we'll be getting in the next couple of months. RDP and Mothur have cropped up on occasion but PANGEA has several reasons why it is better than RDP (last couple of paragraphs of the paper above).
The highlights are that the pipeline is stored and processed on your own site and sequences don't require uploading and the whole pipeline will run from one command.
I was just wondering if anyone out there has had any success/pitfalls with it. I'm currently setting it up to try with some sanger data we have knocking around but some real life experiences would be helpful!