To flash the assembled software into the microcontroller, you need a programmer software and an in-system-programmer.
Atmel Studio allows you to program AVR microcontrollers. In the past, Microchip (formerly Atmel) did produce an USB in-system-programmer, the AVRISP mkII.
Of course there are also third party in-system-programmers available.
RC mode: all fuses keep their default state except the Brown-out detection which is set to 2.7 V:
Quartz mode: all fuses keep their default state except Brown-out detection, CKDIV8 and SUT_CKSEL: