Prepare the pasta per package instructions. Drain and set aside.
Heat the olive oil in a large skillet over medium heat. Add the minced shallots and sauté for about 5 minutes, until they are soft. Add the minced garlic and cook, stirring constantly for 1 minute. Add the drained clams and continue to cook for another 3-4 minutes.
Add the 1/2 cup reserved clam juice, lemon juice, and red pepper flakes to the clam mixture. Bring mixture to a boil, then simmer for 2-3 minutes. Add the hot cooked linguine to the skillet and toss well with the clam sauce. Season with sea salt and freshly cracked pepper, to taste. Top the pasta with Parmesan cheese and chopped parsley. Serve immediately. Enjoy.