Yes, you can provide libraries that you have made yourself. However, we would prefer that we make the libraries so that we have direct control over the uniformity and quality of the libraries going into target capture.
If you send us libraries, they must be compatible with dual-indexed 8bp index reads, and you must make us aware of any incompatibilities within your sample set before you receive a quote.
Please confer with us to make sure that we are fully aware of the type of libraries that you are using, since it is critical to choose the correct adapter-specific blocking oligos during capture and the right amplification primers after capture.