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Add clams to a large bowl and cover with cold water. Add in two teaspoons of salt. Stir and let clams sit for about 10 minutes. Use your hands to remove the clams from the water and into a colander, pour the water and any accumulated sand out. Repeat process two more times.(I like to prep all of my ingredients while the clams soak and make any sides I'll be serving.)
Heat a large pot to a medium heat. Add olive oil. Add 1/2 of the garlic and cook for about 30 seconds to one minute or until it's slightly softened. Be careful not to burn. Add white wine, water and clams. Stir and bring mixture to a boil. Reduce the heat to a simmer and over. Cook for about 8-10 minutes or until the clams open up.
Use a slotted spoon to spoon the clams out. Discard any clams that did not open. Bring the wine mixture to a boil and then reduce to a simmer. Simmer for 4-5 minutes until slightly reduced. Pour liquid into a liquid measuring cup and reserve. Wipe pan clean. Remove all clams from shells and set aside. (If you want a pretty presentation only remove about 3/4 of the clams from the shells.
Bring another large stock pot filling with water to a rolling boil while you cook the rest of the sauce.
Put the same pot you cooked the clams in back over a medium heat. Add butter. Once butter has melted, add shallots, remaining garlic, and crushed red pepper flakes. Season with a little bit of salt and pepper.
Add remaining wine. Bring to a boil and reduce to a simmer. Simmer until reduced by half. Pour the reserved clam and wine mixture in. There may be some sand at the bottom of the mixture, BE CAREFUL TO LEAVE THAT OUT. Bring the mixture to a boil and reduce to a simmer. Simmer until slightly reduced, about 4-5 minutes. Reduce the heat to low.
While the sauce simmers, add the pasta to the boiling water. Cook until just under aldente. Use tongs to transfer the pasta to the sauce, reserve salty cooking liquid. Add lemon zest, parsley, clams, and 1/4 cup of the reserved pasta water. Toss to combine. If needed, add more pasta waster to loosen the sauce up. Season with salt and pepper.
Pour the pasta into a large serving dish, and if you reserved some of the whole clams, nestle them into the pasta. Garnish with chopped parsley.