Place in a bowl and refrigerate until ready to use.
Add shallots and sauté for 5 minutes.
Add garlic and sauté another minute.
Add the chopped tomato, thyme, and red pepper flakes.
Remove mussels from refrigerator and using "kitchen-only" pliers, remove beards.
Add mussels to the pot, cover, reduce heat and simmer until shells open, about 5 to 6 minutes. Discard any unopened mussels.