First step is always to streamline the toolchain to ease development.

There is a wide variety of tools available for writing code, will list these here eventually.

The programming kit I am using is Kanda's STK200-X starter kit, which comes with the AVRISP-U ISP programmer. This programmer has an accompanying Windows AVRISP-U software (download link), which ideally should be linked as an external tool to Microchip Studio for rapid deployment.

./
+-- MYPROG.asmproj
+-- Release   # "Debug" also works
    +-- MYPROG.hex

avrisp-u C:\path\to\MYPROG.asmproj

The USBasp programmer is open source and only requires an ATmega8. This protocol is straightforward to flash with via AVRDUDE. See schematic below:

For Windows, since libusb is a perennial issue, Zadig can be used to quickly install compatible USB drivers which USBASP can interface with. One can get pretty good mileage with libusb-win32.

Note that the usbasp protocol is intended to run at higher speeds, but typical chips require programming speeds of at most 1/4 clock speeds. If the firmware of the usbasp programmer supports it, the clock rate can be reduced by specifying -B in avrdude.

AVRDUDE (Linux, Windows) is a utility program that provides a uniform interface for different hardware programmers on a platform-independent basis. For example, writing a flash program to an ATmega16 chip connected via the USBASP interface only requires the following command:

avrdude -p m16 -c usbasp -U flash:w:[PROGRAM].hex

Some devices may require additional library support from libusb and libftdi1, which is complicated to build from scratch. A working alternative is to use Greuel's fork of AVRDUDE which patches functionality of libusb and libftdi1 to work on Windows.

To get it to work with Kanda's AVRISP-U programmer requires adding the following configuration (adapted from a rather dated 2014 version which mislabels the PID value and adds an extra serial number check), for AVRDUDE 7.0:

avrdude.conf

programmer
  id         = "avrisp-u";
  desc       = "Kanda AVRISP-U FT2232D-based programmer";
  type       = "avrftdi";
  connection_type = usb;
  usbvid     = 0x0403;
  usbpid     = 0x6010;
  usbvendor  = "";
  usbproduct = "";
  usbdev     = "A";
  usbsn      = "";
#ISP-signals - lower ADBUS-Nibble (default)
  reset  = 5;
  sck    = 1;
  mosi   = 2;
  miso   = 3;
#LED SIGNALs - higher ADBUS-Nibble
  pgmled = ~11;
#Buffer Signal - ACBUS - Nibble
  buff   = 6;
;

Now write whatever you want, note write tested using program in Intel hex format:

avrdude -p m16 -c avrisp-u -U flash:w:[PROGRAM].hex

Device USB\VID_0403&PID_6010&MI_00\7&2194c0b3&0&0000 was started.

Driver Name: oem109.inf
Class Guid: {36fc9e60-c465-11cf-8056-444553540000}
Service: FTDIBUS
Lower Filters: 
Upper Filters: 

> avrdude -p m16 -c avrisp-u

E avrftdi_program_enable(889): Device is not responding to program enable. Check connection.
avrdude.exe: initialization failed, rc=-1
             Double check connections and try again, or use -F to override
             this check.

dfu-programmer is only applicable to certain models of chips which already come with a preloaded bootloader, so the chip can be induced into DFU mode to upload software in a non-conflicting flash memory space.

For ease of development, customized header files for the chip for which a program is written for should be used, which provide convenient definitions to chip-specific registers, ports, etc. These are supplied in Microchip Studio (paths below for version 7.0.2594):

• Assembly: C:\Program Files (x86)\Atmel\Studio\7.0\packs\atmel\ATmega_DFP\1.1.130\avrasm\inc\m16def.inc
• C: C:\Program Files (x86)\Atmel\Studio\7.0\toolchain\avr8\avr8-gnu-toolchain\avr\include\avr\iom16a.h

AVRASM2 is the OEM assembler for Atmel chips, which is packaged together with Microchip Studio (supersedes Atmel Studio). File is located at C:\Program Files (x86)\Atmel\Studio\7.0\toolchain\avr8\avrassembler\avrasm2.exe, and compilation can be called with:

avrasm2 -fI -o "MYPROG.hex" -W+ie -i m16def.inc .\MYPROG.asm

The Microchip Studio GUI software itself is actually decently powerful, especially if you have a compatible programmer, and it also includes a simulator for debugging. Supports both C and Assembly.

The main method to retrieve precompiled binaries for AVR-GCC is currently from Microchip website. Otherwise one can also consider building it themselves from the source.

Note that the AVR-AS assembler binary exists, but this should not be called directly, instead using the AVR-GCC compiler to indirectly call the assembler.

sudo apt-get install gcc-avr binutils-avr avr-libc gdb-avr

The STK600 is a development board provided by Atmel, and requires Microchip Studio for operation. Quick start guide for the STK600, instructions reproduced below for STK600-ATMEGA2560 device board (Microchip Studio should be installed):

1. Use mounting screws/clips to secure the chip board (or routing board + chip adapter boards)
   • Ensure the white dot of daughter board is located on the same corner
2. If no external clock, flip the clock switch to INT
3. Connect computer to the USB B port, and switch on the STK600
4. In Microchip Studio, access the STK600 interface tool via Tools > Device Programming > STK600, and select ATmega2560 device and click apply.
5. Under board settings tab, write 3.3V to VTarget (or corresponding to your board)
6. For ISP programming, connect the 6-pin ISP interface and set the ISP frequency to no more than 1/4 of CPU clock frequency. The application can be uploaded from the tool