Check out Dust by Elizabeth Bear. It's set on a generation starship and involves a conflict between different factions and the ship AI.
The two main characters are women and are very interesting. I don't want to
say to much about it, because you find out a lot as the story goes along.
It's the start of a trilogy, but it works well as a standalone book. The next books are Chill (out already) and Grail (out next month).
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