Autopano is a dedicated stitching
program. Stitching is what it does best. But when you shoot photos using RAW formats, you need to do something more to them, something very important: demosaicing.
There are many dedicated RAW conversion programs out there, choosing them is no easy task. I choose RawTherapee
because I am really impressed with the quality it delivers, the speed with which it works, the GUI, and because it's open source and cross platform (Linux, Windows, and possibly soon Mac), so everyone can give it a go and help make it better.
Apart for noise reduction, devignetting, chromatic aberration removal, and countless other filters, the task of a RAW conversion program, above anything else, is to demosaic
your image - that is to take the data from each pixel of the camera sensor, and reconstruct it into a full color image. There are many approaches to doing this, many algorithms, and you should know which one works best for your
camera's sensor. To do that, you must test them yourself. When feeding RAW files directly to Autopano, you do not get to make the choice of which demosaicing algorithm is used, you do not get to remove chromatic aberration nor noise before demosaicing occurs, and other things that should be done at the demosaicing stage, not after stitching.
How much of a problem is this? Take a look at these links, no amount of writing could show you the difference better than pictures:http://rawtherapee.com/forum/viewtopic.php?p=7815#7815
- use this for examining files (only, not for developing them)http://www.linuxphoto.org/html/dcb.html
- more tests