A NextGENe AutoRun template is a file that serves as a starting point for a new job in the NextGENe AutoRun tool. With the exception of the sample files and the output directory folder, an AutoRun template contains all the information and settings that are necessary for an AutoRun job, including reference files, post-processing settings, and so on. Managing NextGENe AutoRun templates consists of creating new AutoRun templates, modifying existing AutoRun templates, and deleting AutoRun templates.