Atmel's SAM-ICE will plug right into the JTAG header, no conversions needed at all. The J-Link universal JTAG will also work, but is much more expensive.
The SAM-ICE is in fact just a J-Link universal device, but locked to just linking and emulating Atmel chips, to allow a lower product price under contract. That's why they also say "J-Link" or "Powered by J-Link".
So whether you want the universal or the Atmel one is mainly down to: Will you possibly or probably also want to sample other brand ARMs in the near future?
On the other hand "If you want to debug, you want a JTAG" is simplified. You can also very comfortably use the Serial connector to pump out std-err, std-out, etc and read those with a terminal program, in effect letting you debug your code just like you'd debug test code on your computer. A very common and doable practise for many low-budget projects, with the added benefit that such constructs will allow you to keep the debugging option in anything you build upon it, wherever it is in the world without that location also needing any special hardware.
If you want to be able to dig into pin-states, add break-points, inspect registers and such without actually modifying your code, THEN you need a JTAG device.
The chip itself has a factory set bootloader section that allows connecting through the first serial hardware block (true for most, if not all larger SAMs) - usually UART0, or an internal USB to be used with a program called SAMBA, which can be downloaded for free from the Atmel website.