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In recent studies, exome sequencing has proven to be a successful screening tool for the identification of candidate genes causing rare genetic diseases. Although underlying targeted sequencing methods are well established, necessary data handling and focused, structured analysis still remain demanding tasks. Here, we present a cloud-enabled autonomous analysis pipeline, which comprises the complete exome analysis workflow. The pipeline combines several in-house developed and publisheddoi:10.1371/journal.pone.0041948 pmid:22870267 pmcid:PMC3411592 fatcat:3kr7xvxdx5gcvkz3rjueqm5zmq