Methods and compositions are provided for enriching for target sequences from a population of nucleic acids, that includes: combining in solution, a population of nucleic acids and a target isolation probe wherein the target isolation probe comprises an affinity binding domain; permitting a single stranded region of the target isolation probe to hybridize to all or a portion of a target sequence in the population of nucleic acids; selectively immobilizing the hybridized nucleic acids from the population containing the target sequences by associating the target isolation probe with a capture domain and removing unbound material; removing non-target sequences from the 3′ end of the target sequence by means of one or more 3′ exonucleases thereby generating a blunt ended duplex or a staggered end at the 3′ end of the target sequence; optionally ligating a 3′ duplex adaptor or a duplex end of a hairpin adaptor to the 3′ end of the target sequence and the 5′ end of the target isolation probe; extending the 3′ end of the target isolation probe to form a blunt end or a staggered end at the 5′ end of the target sequence suitable for ligating and ligating an adapter to the 5′ end of the target sequence and the 3′ extended end of the target isolation probe.