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Pacific Biosciences of California, Inc. Message Board

  • paulieme60 paulieme60 Jan 23, 2014 4:17 PM Flag

    Reducing assembly complexity of microbial genomes with single-molecule sequencing

    Originally Published: 13 September 2013// Updated by Next-Generation-Sequencing on Jan. 22, 2014
    Originally Published: 13 September 2013// Updated by Next-Generation-Sequencing on Jan. 22, 2014

    Reducing assembly complexity of microbial genomes with single-molecule sequencing
    Abstract
    Background
    The short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant resources required to manually close gaps in draft assemblies. Third-generation, single-molecule sequencing addresses this problem by greatly increasing sequencing read length, which simplifies the assembly problem.
    Results
    To measure the benefit of single-molecule sequencing on microbial genome assembly, we sequenced and assembled the genomes of six bacteria and analyzed the repeat complexity of 2,267 complete bacteria and archaea. Our results indicate that the majority of known bacterial and archaeal genomes can be assembled without gaps, at finished-grade quality, using a single PacBio RS sequencing library. These single-library assemblies are also more accurate than typical short-read assemblies and hybrid assemblies of short and long reads.
    Conclusions
    Automated assembly of long, single-molecule sequencing data reduces the cost of microbial finishing to $1,000 for most genomes, and future advances in this technology are expected to drive the cost lower. This is expected to increase the number of completed genomes, improve the quality of microbial genome databases, and enable high-fidelity, population-scale studies of pan-genomes and chromosomal organization.

 
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