title: Whole Genome Sequence of Xylaria
design: A sequence of nucleotides incorporated by the DNA polymerase while reading a template, such as a circular SMRTbell (TM) template. Polymerase reads are most useful for quality control of theinstrument run. Polymerase read metrics primarily reflect movie length and other run parametersrather than insert size distribution. Polymerase reads are trimmed to include only the high qualityregion; they include sequences from adapters; and can further include sequence from multiplepasses around a circular template.Each polymerase read is partitioned to form one or more subreads, which contain sequence froma single pass of a polymerase on a single strand of an insert within a SMRTbell (TM) template andno adapter sequences. The subreads contain the full set of quality values and kinetic measurements.Subreads are useful for de novo assembly.In the case of Illumina data, the sequencing library is prepared by random fragmentation of theDNA or cDNA sample, followed by 5 and 3 adapter ligation. This library is loaded into a flow cellwhere fragments are captured on a lawn of surface-bound oligos complementary to the libraryadapters. As all 4 reversible, terminator-bound dNTPs are persent during each sequencing cycle,natural competition minimizes incorporation bias and greatly reduces raw error rates compared toother technologies. Then, sequencing data is converted into raw data for the analysis.