Optimally you want some form of litter in the run to allow for poop clean up/comspoting and to manage mud. Most popular choices are probably deep litter and sand, though what works best for you will depend on your location, your flock density, your run set up, run management, etc. Sand tends to work well if your run stays dry most of the time and you're able to regularly scoop poop. Deep litter tends to work better if rain/mud is an issue.