In our latest poll that started mid of November 2011 we raised the question about your sequencing strategies for scaffolding projects. 29 ngs-expert.com readers did submit their votes.
39% of all votes agree my own opinion that LPE and LJD libraries are the preferred method for scaffolding of contigs. Long reads of up to 40 kbp can be easily and efficiently bridged.
But despite that, it is also obvious that all other techniques are still used for scaffolding projects. And I am still interested to see whether this might change with the new C2 chemistry for PacBio RS that is announced for Q1.