Start by finely dicing the red onion and soaking it in cold water while you prepare the salsa. This will help cut the harsh bite of the onion flavor a little, minimizing its aftertaste.
Set up your food processor and with the blade spinning, add the garlic clove. Once it has been chopped finely, add the cilantro leaves through the feed tube. Once the cilantro leaves are chopped, add the chipotle pepper. Then, stop the processor and add the tomatoes, salt and lime juice to taste (start with half a lime and add more if needed). Process until the salsa is the texture you like.
Add the minced Jalapeño pepper. Drain the onion well and add it to the processor as well. Process one more time. Adjust the seasonings (salt and lime juice) to taste and serve with tortilla chips.