Schematic representation of the pipeline’s architecture. Interaction with the system happens through a Galaxy-based GUI: after logging in to the web site, the user is able to upload data and customize the various parameters using a dedicated subsection of the Galaxy tool panel (1). Although each pipeline step can be run as a stand-alone tool, Galaxy also allows to combine them in a single workflow, thus enabling the automation of the entire process. When the user submits a job, Galaxy transfers all parameters chosen via the GUI to a driver script (2), which schedules the actual computation on the computing cluster (3). In the case of the alignment and filtering step, actual processing is further delegated to Hadoop (4), while the driver script acts as a final output collector. Finally, job output is returned to the graphical front end (5) that presents final results to the user (6).