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Place rinsed, scrubbed clams in a deep saucepan over high heat, and cover. Cook for a few minutes, then add the thyme, garlic, onion, and wine and cook for another 5 minutes shaking the pan from time to time. Transfer the open clams to a bowl using a slotted spoon. Discard the liquid and any clams that have not opened.
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When they have cooled down pry the shells open and remove the flesh, transferring it to another bowl. Place the clam shells in a shallow roasting pan.
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Preheat the oven to 350° F or 170° C.
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Make the filling: In a frying pan over medium heat warm the olive oil, garlic, and onion and cook for a few minutes until the onion becomes translucent.
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Add the wine, and cook until the alcohol evaporates. Add the stock. Cook until the liquid is reduced by half. Remove the skillet from the heat and add the bread crumbs, lemon juice, and the reserved clams.
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Mix it all together and spoon the filling back into the clam shells, making sure that there is at least one clam for every shell.
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Make the topping: Mix all the ingredients together in a bowl and divide it among the shells, over the filling.
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Bake for about 15 minutes, until the tops are golden. Serve with lemon wedges