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SW4STM32 and SW4Linux fully supports the STM32MP1 asymmetric multicore Cortex/A7+M4 MPUs

   With System Workbench for Linux, Embedded Linux on the STM32MP1 family of MPUs from ST was never as simple to build and maintain, even for newcomers in the Linux world. And, if you install System Workbench for Linux in System Workbench for STM32 you can seamlessly develop and debug asymmetric applications running partly on Linux, partly on the Cortex-M4.
You can get more information from the ac6-tools website and download (registration required) various documents highlighting:

System Workbench for STM32


Access ETM of Nucleo F401RE without using a debug kit

Ok, now you give little more details but still lot of things remain unknown.
First of all, the board of Nucleo-F401RE comes with built-in debugger, which connect the debug interface of STM32F401 via SWD, and the USB interface to your host. Other than that, the composite USB also provides mass storage device and virtual serial port, which connect to one of USART port on STM32F401.
When you said downloading the firmware through the usb interface, I guess you are talking about to use ST-Link utility program running on your PC? Or inside of Atollic TrueStudio through the OpenOCD->SWD debugger?
It seems like you should spend little more time to read the “user’s manual for Nucleo-F401RE”, and the schematic to the board, and maybe the datasheet of STM32F401? That is the big picture I’m talking about.
-Andy