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In a wide sauté pan, heat 1 tablespoon of olive oil over medium heat. Add the garlic, red pepper flakes, and parsley stems. Sauté until fragrant, about 1 minute.
Add the clams and pour in the Vermentino di Gallura DOCG. Cover and cook for 5–7 minutes, or until the clams open. Discard any that remain closed. Strain the clam liquid through a fine mesh sieve and reserve. Remove most of the clams from their shells, keeping a few whole for garnish.
In a clean pan, heat 1 tablespoon of olive oil over medium heat. Add the fregola and toast for about 2 minutes, stirring frequently, until lightly golden and aromatic. Add the reserved clam liquid and passata, stirring to combine.
Cook the fregola risotto-style by adding warm water or fish stock a ladle at a time, stirring frequently and allowing each addition to absorb before adding more. Continue this process for 15–18 minutes, or until the fregola is tender with a slight bite. Season with salt to taste.
Fold in the shelled clams and chopped parsley. Finish with a drizzle of extra virgin olive oil. Plate the fregola, top with the whole clams, and grate Bottarga di Muggine IGP generously over the top just before serving.