Abstract
Second generation sequencing (SGS) technologies revolutionized the field of genomics, transcriptomics and epigenomics. These technologies generate massive amounts of data at modest cost. While the introduction of second-generation sequencing reduced per-nucleotide cost of DNA sequencing, whole genome finishing currently remains prohibitively expensive. The single molecule, real time (SMRT) DNA sequencing (Eid et al, 2009) offers potential advantages over other current sequencing technologies for its faster turnaround time, lower cost, and longer read lengths. Unlike SGS, single molecule sequencing does not rely on PCR and thus overcomes biases related to phasing and PCR amplification. However, sequencing DNA molecules in its native state imposes other challenges associated with possible impurities present in the sample preparation. While the purity of the DNA fragment library is important for good quality sequencing using any sequencing technology, SMRT technology is highly sensitive to carryover impurities introduced during library construction. Here, we demonstrate how impurities present in a commonly used DNA library protocol impact sequencing performance on PacBio.