Hi Marco,
Yes, it's an application called called Bossa: GitHub - shumatech/BOSSA: BOSSA is a flash programming utility for Atmel's SAM family of flash-based ARM microcontrollers. The motivation behind BOSSA is to create a simple, easy-to-use, open source utility to replace Atmel's SAM-BA software. BOSSA is an acronym for Basic Open Source SAM-BA Application to reflect that goal..
The Arduino IDE also uses Bossa to upload binaries to your board over its native USB port, but it's working in the background.