I don't think there is ever a direct refutation of religion in the Sequences, but if you read all of them, you will find yourself much better equipped to think about the relevant questions on your own.

EY is himself an Atheist, obviously, but each article in the Sequences can stand upon its own merit in reality, regardless of whether they were written by an atheist or not. Since EY assumes atheism, you might run across a couple examples where he assumes the reader is an atheist, but since his goal is not to convince you to be an atheist, but rather, to be aware of how to properly examine reality, I think you'd best start off clicking ‘Sequences" at the top right of the website.