How long will it take?

The queue for a short-insert, well made library is usually a couple of weeks (and could be less than one week for MiSeq runs). The queue for a library with long inserts which is poorly made or which has a wide range of insert sizes can be over a month, especially if there needs to be effort spent on getting it into a useable condition.
We QC using the Fragment Analyzer and if there are concerns at this point we contact you immediately. The sooner you can respond and help with any adjustments, the quicker the sample can move to the next step.