Captured sequences

[suludana]

Hi all,
I want to sequence Nimblegen captured sequences on an Illumina GA. These fragments have approximately 500 bp.

I have to generate smaller fragments (more appropriate to Illumina GA) and to eliminate the specific Nimblegen linkers sequence from the reads.
Nimblegen recommends catenation of the library inserts (captured fragments) followed by sonication.

I´m thinking about a direct DNAse digestion of the captured fragments (until a 100-150 bp size) followed by the standard sample preparation protocol.

Does anyone have experience in this subject? ¿Someone can give me an opinion?

Thanks