You can use the NextGENe AutoRun tool to carry out the batch processing of previously processed sequence alignment projects and export outputs of your choosing. This option is particularly helpful in the event that you have multiple projects that have been run without post-processing options as it prevents you from having to reprocess each project individually or having to load each project in the NextGENe Viewer and manually exporting the post-processing options through the viewer. Batch processing previously processed projects is a three step process. First, you must create the needed report Settings files (.ini files) and then load all these files on the post-processing page of the Project Wizard to save a single Settings file that contains all the settings for all the selected reports and outputs. Second, you must load the projects and this single Settings file. Third, you must specify the settings to run the job.