The Orphans Trilogy, by Sean Williams and Shane Dix

Echoes of Earth, Orphans of Earth, Heirs of Earth

Sean Williams and Shane Dix re-unite after their excellent Evergence trilogy.

Like the Evergence trilogy, this is set in a "real" future, where there are Powers (with a capital P) beyond the ken of man.

The series is full of flawed characters (seriously flawed in many cases, since they're essentially buggy programs) trying to overcame major adversity (ok, the destruction of Earth and almost all real humans is pretty adverse).

Highly recommended.