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Pacific Biosciences of California, Inc. Message Board

  • paulieme60 paulieme60 Oct 1, 2013 5:22 PM Flag

    PacBio sequence data has a higher degree of accuracy than an Illumina !!!

    An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome
    Published: 1 October 2013
    Abstract (provisional)
    Background
    Second generation sequencing has permitted detailed sequence characterisation at the whole genome level of a growing number of non-model organisms, but the data produced have short read-lengths and biased genome coverage leading to fragmented genome assemblies. The PacBio RS long-read sequencing platform offers the promise of increased read length and unbiased genome coverage and thus the potential to produce genome sequence data of a finished quality containing fewer gaps and longer contigs. However, these advantages come at a much greater cost per nucleotide and with a perceived increase in error-rate. In this investigation, we evaluated the performance of the PacBio RS sequencing platform through the sequencing and de novo assembly of the Potentilla micrantha chloroplast genome.
    Results
    Following error-correction, a total of 28,638 PacBio RS reads were recovered with a mean read length of 1,902bp totalling 54,492,250 nucleotides and representing an average depth of coverage of 320x the chloroplast genome. The dataset covered the entire 154,959bp of the chloroplast genome in a single contig (100% coverage) compared to seven contigs (90.59% coverage) recovered from an Illumina data, and revealed no bias in coverage of GC rich regions. Post-assembly the data were largely concordant with the Illumina data generated and allowed 187 ambiguities in the Illumina data to be resolved. The additional read length also permitted small differences in the two inverted repeat regions to be assigned unambiguously.
    Conclusions
    This is the first report to our knowledge of a chloroplast genome assembled de novo using PacBio sequence data. The PacBio RS data generated here were assembled into a single large contig spanning the P. micrantha chloroplast genome, with a higher degree of accuracy than an Illumina dataset ge

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