NextGENe's AutoRun Tool allows users to quickly set up job files to specify sample files, reference files and settings for the analysis of multiple projects. The NextGENe AutoRun Tool includes a Job Editor to allow the creation of job files using point-and- click operation within a single step. NextGENe AutoRun scans the job files to check for the availability of all files needed for processing a job. When files are available, NextGENe AutoRun launches NextGENe to begin processing the job. Jobs are processed consecutively unattended. If some files are not available, NextGENe AutoRun will periodically re-check for the files at the time interval specified in the NextGENe AutoRun settings. Job files can be easily edited to add additional jobs or edit jobs that have not yet been processed. Also, additional jobs can be added to the queue while NextGENe is currently processing another set of jobs. NextGENe will automatically begin the next list of jobs that are queued once the first list is complete.