In a large pot, bring 10 cups of water to a boil. Add beef shank and brisket, and simmer for 2 hours until meat is tender.
Remove the meats from the pot, let cool, then slice thinly. Return the bones to the pot to continue simmering.
Add lemongrass, onion, fish sauce, sugar, and salt to the pot. Simmer for another hour.
In a small pan, heat annatto seed oil over medium heat. Add minced garlic, minced lemongrass, and chili flakes. Cook until fragrant, then add to the soup pot.
Prepare rice vermicelli noodles according to package instructions.
Assemble the soup by placing a portion of noodles in each bowl, topping with sliced beef, and ladling hot broth over the top.
Garnish with cilantro, green onions, a wedge of lime, bean sprouts, and Thai basil leaves.