It is hard to get the yeast genome sequence with PacBio due to the ribosome and some other DNA binding proteins that inhibit the polymerase, any suggestions for improvement?
Maybe try a MagBead clean-up in stead of a traditional AMPure clean-up?http://www.smrtcommunity.com/servlet/servlet.FileDownload?file=00P7000000HYLjREAX
You should try to get genomic DNA of better quality instead of trying to purify DNA of marginal purity.. We used the Gentra kit from Qiagen to extract S. Cerevisae and S. Pombe DNA and got great PacBio data